ABOUT THIS PROSPECTUS

This prospectus is part of a registration statement on Form S-3 that we filed with the Securities and Exchange Commission, or the SEC, on July [    ], 2013, pursuant to which the selling stockholdersSeptember 12, 2014, using a “shelf” registration process. Under this shelf registration process, we may, sell or otherwise dispose up to 20,500,000 shares of our common stock, including 12,500,000 shares of our common stock issuable upon the exercise of warrants, from time to time. We will not receivetime, sell any combination of the proceedssecurities described in this prospectus in one or more offerings up to the aggregate amount of $50,000,000. In addition, the selling warrant holder may offer and sell, from these sales, excepttime to time, up to 70,000 warrant shares, in one or more offering and at prices and on terms that upon any exerciseit determines at the time of the warrants by payment of cash, we will receive the exercise priceoffering, as described in this prospectus.

This prospectus provides you with a general description of the warrants. We have agreedsecurities we may offer and the warrant shares the selling warrant holder may offer. A prospectus supplement may add to, pay certain expensesupdate or change information contained in this prospectus, and, accordingly, to the extent inconsistent, information in this prospectus is superseded by the information in any prospectus supplement.

A prospectus supplement may describe, as applicable: the terms of the securities offered by us or the selling warrant holder; the initial public offering price; the price paid for the securities; net proceeds; and the other specific terms related to the registrationoffering of the shares of common stock pursuant to the registration statement of which this prospectus forms a part.securities.

You should rely only on the information that we have provided or incorporated by reference in this prospectus, any applicable prospectus supplement and any related free writing prospectus that we may authorize to be provided to you. WeNeither we nor the selling warrant holder have not authorized anyone to provide you with different information. No dealer, salesperson or other person is authorized to give any information or to represent anything not contained in this prospectus or any applicable prospectus supplement or any related free writing prospectus that we or the selling warrant holder may authorize to be provided to you. You mustIf anyone provides you with different or inconsistent information, you should not rely on any unauthorized information or representation.it. You should assume that the information in this prospectus, any applicable prospectus supplement or any related free writing prospectus is accurate only as of the date on the cover of the document and that any information we have incorporated by reference is accurate only as of the date of the document incorporated by reference, regardless of the time of delivery of this prospectus, any applicable prospectus supplement or any related free writing prospectus, or any sale of a security.  Our business, financial condition, results of operations and prospects may have changed since that date.those dates.

This prospectus contains summaries of certain provisions contained in some of the documents described herein, but reference is made to the actual documents for complete information. All of the summaries are qualified in their entirety by the actual documents. The registration statement containing this prospectus, including exhibits to the registration statement, provides additional information about us and the securities offered under this prospectus. Copies of some of the documents referred to herein have been filed, will be filed or will be incorporated by reference as exhibits to the registration statement of which this prospectus is a part, and you may obtain copies of those documents as described below under the heading “Where You Can Find Additional Information.”

We urge you to carefully read this prospectus, any applicable prospectus supplement, together with the information incorporated herein by reference as described under the heading “Where You Can Find Additional Information.”

SUMMARY

i

SUMMARY

This summary highlights selectedcertain information contained in greater detail elsewhere in this prospectus or incorporated by reference ininto this prospectus,prospectus. This summary is not complete and does not contain all of the information that you needshould consider before deciding whether to considerinvest in making your investment decision.our securities. You should carefully read the entirethis prospectus, the applicableany accompanying prospectus supplement andsupplements, any related free writing prospectus that we have authorized for use in connection with this offering and the documents incorporated by reference herein and in any accompanying prospectus supplement, including the risks of investinginformation referred to under the heading “Risk Factors” in our common stock discussedthis prospectus on page 5, under the heading “Risk Factors” contained in the applicable prospectus supplement and any related free writing prospectus, and under similar headings in the other documents that are incorporated by reference into this prospectus. You should also carefully read the information incorporated by reference into this prospectus including our financial statements, and the exhibits to the registration statement of which thisany prospectus is a part.supplement. Unless otherwise mentioned or unless the context requires otherwise, all references in this prospectus to “Vermillion,” “the company,” “we,” “us,” “our” or similar references mean Vermillion, Inc. together with its consolidated subsidiaries.

Vermillion, Inc.

Our Company

Our vision is to become a recognized leaderdrive advancement in the advancement of women’spersonalized medical management — initially focused on ovarian health by providing innovative methods that detect, monitor— to improve outcomes for patients, physicians and manage the treatment of gynecologic cancers.providers.

We are dedicated to the discovery, development and commercialization of novel high-value diagnostic tests that help physicians diagnose, treat and improve outcomes for patients. Our testsOVA1® ovarian tumor triage test (“OVA1”) and soon-to-be-marketed CA 125II test are intended to detect, diagnose and stage disease, and to help guide decisions regarding prognosis and patient treatment. Thesetreatment, which may include decisions to refer patients to specialists, to perform additional testing, or to assist in the selection or monitoring of therapy and disease progression.response to therapy. A distinctive feature of our approach is to combine multiple biomarkersmarkers into a single, reportable index score that has higher diagnostic effectivenessaccuracy than its constituents.

We concentrate on our development of novel diagnostic tests in the fields of gynecologic oncology and women’s health, with thean initial focus on ovarian cancer. We also intend to address clinical questions related to early disease detection, treatment response, monitoring of disease progression, prognosis and other issues in the fields of oncology and women’s healthothers through collaborations with leading academic and clinical research institutions.

Our lead product, OVA1, an ovarian canceris a blood test was cleared by thedesigned to identify women who are at a high risk of having a malignant ovarian tumor prior to surgery. The United States Food and Drug Administration (“FDA”(the “FDA”) cleared OVA1 in September 2009. 2009, and we commercially launched OVA1 in March 2010.

On June 23, 2014, Vermillion launched ASPiRA LABS, which specializes in applying biomarker-based technologies, including OVA1, to address critical needs in the management of gynecologic cancers. ASPiRA LABS provides expert diagnostic processing and results using a state-of-the-art biomarker-based diagnostic algorithm to inform clinical decision making and advance personalized treatment plans. In addition, ASPiRA LABS, a national lab based near Austin, Texas, seeks to serve as an educational and resource hub for healthcare professionals and women facing surgery for ovarian masses that are potentially cancerous and related gynecologic conditions. The lab currently processes our OVA1 test, a diagnostic test and clinical decision aid for women’s health in ovarian cancer, and we expect the lab to process the CA 125II test in the future. We plan to expand the testing provided by the lab to other gynecologic conditions with high unmet need.  We also plan to develop and perform at ASPiRA LABS laboratory-developed tests (“LDTs”). ASPiRA began accepting samples on June 23, 2014.  ASPiRA currently holds a Certificate of Registration under the Clinical Laboratory Improvement Amendments of 1988 (“CLIA”) and a state laboratory license in California. ASPiRA is in the process of obtaining state licensure in New York, Florida, Rhode Island, Maryland and Pennsylvania.

We are focused on the execution of four core strategic business drivers in ovarian cancer diagnostics to build long-term value for our investors:

We believe that these business drivers will contribute significantly to addressing unmet medical needs for women faced with ovarian cancer and the continued development of our business.

Our Product

OVA1 addresses a clear unmet clinical need, namely the pre-surgical identification of women who are at high risk of having a malignant ovarian tumor. Numerous studies have documented the benefit of referral of these women to gynecologic oncologists for their initial surgery. Prior to the clearance of OVA1, no blood test had been cleared by the FDA for physicians to use in the pre-surgical management of ovarian adnexal masses. OVA1 is a qualitative serum test that utilizes five well-established biomarkers and proprietary FDA-cleared software cleared as part of the OVA1 510(k) to determine the likelihood of malignancy in women over age 18, with a pelvic mass for whom surgery is planned. OVA1 should not be used without an independent clinical/radiological evaluation and is not intended to be a screening test or to determine whether a patient should proceed to surgery. Incorrect use of OVA1 carries the risk of unnecessary testing, surgery and/or delayed diagnosis. OVA1 was developed through large clinicalpre-clinical studies in collaboration with numerous academic medical centers encompassing over 2,500 clinical samples. OVA1 was fully validated in a prospective multi-center clinical trial encompassing 27 sites reflective of the diverse nature of the clinical centers at which ovarian adnexal masses are evaluated. The results of the clinical trial demonstrated that in a clinical cohort of 516 patients, OVA1, in conjunction with clinical evaluation, was able to identify 95.7% (154/161) of the malignant ovarian tumors overall, and to rule out malignancy with a negative predictive value (“NPV”) of 94.6% (123/130). At the 2010 International Gynecologic Cancer Society Meeting, data were presented demonstrating the high sensitivity of OVA1 for epithelial ovarian cancers; OVA1 detected 95/96 epithelial ovarian cancer cases for a sensitivity of 99.0%, including 40/41 stage I and stage II epithelial ovarian cancers, for an overall sensitivity of 97.6% for early stage epithelial ovarian cancers, as compared to 65.9% for CA125 using the American College of Obstetricians and Gynecologists (“ACOG”) cutoffs. The improvement in sensitivity was even greater among premenopausal women; for OVA1, sensitivity for early stage epithelial ovarian cancer was 92.9% and for CA125, sensitivity was 35.7%. Overall, OVA1 detected 76% of malignancies missed by CA125, including all advanced stage malignancies. OVA1 is not indicated for use as a screening or stand-alone diagnostic assay.

In 2012, we completed a second pivotal clinical study of OVA1 called the “OVA500 study” andstudy,” led by Dr. Robert E. Bristow, Director of Gynecologic Oncology Services with UCUniversity of California Irvine Healthcare. The study evaluated OVA1 diagnostic performance in a population of 494 evaluable patients who underwent surgery for an adnexal mass after enrollment by a non-gynecologic oncologist,oncologist. In February 2013, the intended use population for routine OVA1 testing. In the new study, of the 27 sites used in each study, only 10 were common to both. Collectively, the clinical trial and the OVA 500 study evaluated 1,110 eligible subjects at a total of 44 sites. Despite the difference in population between the two studies, and the large number of differing sites, the sensitivity of OVA1 added to clinical impression (also called OVA1 dual assessment) was identical, at 95.7% (88/92). In addition, overall NPV of OVA1 dual assessment was 98.1% (204/208), higher than the 94.6% NPV found in the earlier validation study. In premenopausal surgery patients, OVA1 dual assessment sensitivity was 93.5% (29/31), NPV was 98.6% (145/147) and specificity was 58.9% (145/246) when combined with clinical assessment. OVA1 also showed strong performance in detecting early stage malignancies. OVA1 correctly stratified 91.4% (32/35) of early stage cancers and 89.3% (25/28) of stage I cancers as high risk, respectively. In comparison, CA125-II sensitivity was 65.7% (23/35) for early stage and 64.3% (18/28) for stage I malignancies. Overall, the results strongly and independently confirmed the clinical performance of OVA1 in presurgical triage of adnexal mass patients, including premenopausal and early stage cancers.

The OVA500 study was published in February 2013 in the peer-reviewed journalGynecologic Oncology, which we believe enjoys the highest impact factor rating of any journal worldwide focused on gynecologic oncology. The results have also been incorporated into an updated Medical Education presentation, as well as our Marketing and Reimbursement collateral. Since many professional medical societies stress the importance of multiple independent clinical trials as so-called “evidence levels”, we also believe that the OVA500 study contributes to a higher evidence level relative to OVA1’s utility in the medical management of adnexal masses.

In addition to these pivotal studies, three follow-on studies have been published bringing the number of full research articles on OVA1 clinical performance to a total of five peer-reviewed publications. Together, we believe these data provide strong clinical evidence that OVA1, in conjunction with the physician’s independent clinical and radiological evaluation, improves the pre-surgical detection of ovarian cancer, across all stages or subtypes, in patients undergoing surgery for a suspicious ovarian mass.

The American Medical Association Current Procedural Terminology (“CPT®”) Panel approved a Category I CPT code (81503) for OVA1, which became effective in January 2013.

Dr. Bristow publishedpresented another study at the Society of Gynecological Oncology (“SGO”) in March 2013 which was published in the journal Obstetrics and& Gynecology (the(also known as the Green Journal) in June 20132013.  This study was based on the medical records of 13,321 women with epithelial cancer, the most common type of ovarian cancer, diagnosed from 1999 to 2006 in California. Only 37 percent of these patients received treatment that adhered to guidelines set by the National Comprehensive Cancer Network (“NCCN”), an alliance of 2123 major cancer centers with expert panels that analyze, research and recommend cancer treatments.

The study found that surgeons who operated on 10 or more women a year for ovarian cancer, and hospitals that treated 20 or more a year, were more likely to stickadhere to theNCCN guidelines and their patients lived longer. Among women with advanced disease — the stage at which ovarian cancer is usually first found — 35 percent survived at least five years if their care met the guidelines, compared with 2526 percent of those whose care fell short.

According to Dr. Bristow, principal investigator of the study, “If we could just make sure that women get to the people who are trained to take care of them, the impact would be much greater than that of any new chemotherapy drug or biological agent.” (NY Times, March 11,

In May 2013, Denise Grady)

On June 11, 2013, we announced that OVA1 receivedSGO issued a new position statement on clinical validation and medical use issued by the Society of Gynecologic Oncology (SGO). Citing peer-reviewed publications from two pivotal clinical studies of OVA1 versus standard of care, the statement also referred to OVA1 use within the context of the American Congress of Obstetricians and Gynecologists’ (ACOG) 2011 Committee Opinion, “The Role of the Obstetrician-Gynecologist in the Early Detection of Epithelial Ovarian Cancer.” This guideline, updated from a previous version issued in 2002, covers the management of adnexal masses, including serum markers for ovarian cancer detection.OVA1. This second SGO statement on OVA1 since its FDA clearance in 2009 represents another significant step toward acceptance of OVA1 as the standard of care for pre-surgically evaluating the risk of ovarian cancer in women with adnexal masses.   The statement, titled “Multiplex Serum Testing for Women with Pelvic Mass”, reads:

Current“Blood levels of five proteins in women with a known ovarian mass have been reported to change when ovarian cancer is present. Tests measuring these proteins may be useful in identifying women who should be referred to a gynecologic oncologist. Recent data have suggested that such tests, along with physician clinical assessment, may improve detection rates of malignancies among women with pelvic masses planning surgery. [1],[2] Results from such tests should not be interpreted independently, nor be used in place of a physician’s clinical assessment. Physicians are strongly encouraged to reference the American Congress of Obstetricians and former academic and research institutionsGynecologists’ 2011 Committee Opinion “The Role of the Obstetrician-Gynecologist in the Early Detection of Epithelial Ovarian Cancer” to determine an appropriate care plan for their patients. It is important to note that we haveno such test has been evaluated for use as, nor cleared by, the FDA as a screening tool for ovarian cancer. SGO does not formally endorse or have had collaborations with includepromote any specific products or brands.”

[1] Bristow RE, Smith A, Zhang Z, Chan DW, Crutcher G, Fung ET, et al. Ovarian malignancy risk stratification of the adnexal mass using a multivariate index assay. Gynecol Oncol 2013;128: 252–259

[2] Ueland FR, Desimone CP, Seamon LG, Miller RA, Goodrich S, Podzielinski I, et al. Effectiveness of a multivariate index assay in the preoperative assessment of ovarian tumors. Obstet Gynecol 2011;117:1289-1297.

We believe the position statement does two things: 

In June 2013 our collaborators from Johns Hopkins University SchoolBiomarker Discovery and Translation Center presented data from “proof of Medicine (“JHU”);concept” work to identify markers with high clinical specificity that may complement OVA1. These results were presented in a poster at the Universityannual meeting of Texas M.D. Anderson Cancer Center (“M.D. Anderson”); University College London (“UCL”); the UniversityAmerican Society for Clinical Oncology by Dr. Zhen Zhang and co-workers. The study identified a set of Texas Medical Branch (“UTMB”);5 biomarkers (CA125, prealbumin, IGFBP2, IL6 and FSH) which optimally reduced false positives among a targeted set of OVA1-positive benign patients. This panel was subsequently tested in a 50/50 cross-validation strategy against a sampling of OVA500 patients (N=384), to evaluate specificity and other diagnostic parameters. At a fixed sensitivity of 90%, the Katholieke Universiteit Leuven; Clinicmedian specificity of Gynecologymodels using the new panel in testing was 80.6%. The mean and Clinicmedian absolute improvements over that of Oncology, Rigshospitalet, Copenhagen University Hospital (“Rigshospitalet”);OVA1 were 18.6% and 20.3%, respectively. The new panel demonstrated the Ohio State University Research Foundation (“OSU”); Stanford University (“Stanford”);possibility to improve specificity over that of the existing OVA1 algorithm, while maintaining a high sensitivity in pre-surgical assessment of malignancy. The work will be submitted for publication in 2014.

We are in the process of identifying intended use(s) and establishing a regulatory or commercial pathway for a potential next-generation OVA product utilizing this or another new panel. Any actual product development will likely differ significantly depending on a number of technical and commercial factors.

A study published in July 2014 in The American Journal of Obstetrics & Gynecology, examined the relationship between two imaging methods, ultrasound and computed tomography, and the UniversityOVA1 test result in assessing the risk of Kentuckyovarian cancer among patients planning surgery for an ovarian mass. Using data obtained from 1,100 ovarian mass surgery patients in two previous pivotal trials of OVA1’s clinical performance, conducted in 2007 and 2012, the study found that adding OVA1 reduced the number of ovarian cancers missed with imaging alone by 84-90%. Specifically, ultrasound alone missed 23.1% of ovarian cancers that were presented, but when OVA1 was added in parallel, the number of ovarian cancers missed decreased to 2.2%. When CT was used alone, 20.2% of ovarian cancers were missed but this rate fell to 2.9% when OVA1 was added in parallel. Additionally, the study found that when ultrasound and OVA1 were combined in parallel, 95% of ovarian cancers in a subgroup of early-stage patients were detected.

Novitas Solutions (formerly Highmark Medicare Services), a Medicare contractor, covers and reimburses for OVA1. In December 2013, the Centers for Medicare and Medicaid Services (“UK”CMS”). made its final determination and authorized Medicare contractors to set prices for Multianalyte Assays with Algorithmic Analyses(“MAAA”) test CPT codes when they determine it is payable. CMS also validated that an algorithm has unique value by specifying that the gap-fill process and not cross-walk should be used by contractors to price MAAA tests. We expect OVA1 to be priced using the gap-fill method. We will be engaged in that process in 2014 for pricing effective January 1, 2015. This decision also sets a precedent for recognizing the value of biomarker developed tests to clinical decision-making and healthcare efficiencies.

Independent BlueCross BlueShield plans representing approximately 8.0 million lives provide coverage for OVA1. In total, including Medicare and other private payers, approximately 55.5 million patients have access to and coverage for OVA1. 

Under the terms of our Strategic Alliance Agreement with Quest Diagnostics Incorporated (“Quest Diagnostics”), which we terminated in August 2013, Quest Diagnostics was required to pay us a fixed payment of $50 per OVA1 test performed, as well as 33% of its “gross margin” from revenue from performing OVA1 tests domestically, as that term is defined in the Strategic Alliance Agreement. Prior to the termination of the agreement, Quest Diagnostics had the right to be the exclusive clinical reference laboratory marketplace provider of OVA1 tests in its exclusive territory, which included the US, Mexico, the United Kingdom and India. This right extended through September 11, 2014, and Quest Diagnostics had the right to extend its exclusivity period for an additional year on the same terms and conditions. In August 2013, we sent Quest Diagnostics a notice of termination. Notwithstanding the termination, we agreed that Quest Diagnostics could continue to make OVA1 available to healthcare providers on the same financial terms following the termination while negotiating in good faith towards an alternative business structure. Quest Diagnostics has disputed the effectiveness of our notice of termination.

Corporate Information

We were originally incorporated in California on December 9, 1993, under the name Abiotic Systems. In March 1995,and we changed our corporate name to Ciphergen Biosystems, Inc. and in May 2000, we reincorporated in Delaware. We had our initial public offering in September 2000. On November 13, 2006, we sold assetsOur executive offices are located at 12117 Bee Caves Road, Building Three, Suite 100, Austin, TX 78759, and liabilitiesour telephone number is (512) 519-0400. We maintain websites at www.vermillion.com and www.aspiralab.com where general information about us is available. Our websites, and the information contained therein, are not a part of our protein research tools and collaborative services business (the “Instrument Business Sale”), to Bio-Rad Laboratories, Inc. (“Bio-Rad”), in order to concentrate our resources on developing clinical protein biomarker diagnostic products and services. On August 21, 2007, we changed our corporate name to Vermillion, Inc. On March 30, 2009, we filed a voluntary petition for relief under Chapter 11 of Title 11 of the United States Code (the “Bankruptcy Code”) in the United States Bankruptcy Court for the District of Delaware (the “Bankruptcy Court”). Subsequently, on January 22, 2010, the confirmation order issued by the Bankruptcy Court approving our Second Amended Plan of Reorganization under Chapter 11 dated January 5, 2010 became final and all conditions precedent to January 22, 2010 were satisfied or waived. Accordingly, we emerged from bankruptcy protection under Chapter 11 on January 22, 2010. Our Bankruptcy case was formally closed on January 19, 2012.this prospectus.

RISK FACTORS

RISK FACTORS

Investing in shares of our common stocksecurities involves a high degree of risk. Before making an investment decision, you shouldPlease carefully consider the risksrisk factors described under “Risk Factors” in any applicable prospectus supplement and in our most recent Annual Report on Form 10-K, or any subsequent updates in our Quarterly Reports on Form 10-Q together with all of the other information appearing in or incorporated by reference into this prospectus and any applicable prospectus supplement, before deciding whetherother filings we make with the SEC pursuant to purchase any of the common stock being offered. Our business, financial conditionSection 13(a), 13(c), 14 or results of operations could be materially adversely affected by any of these risks. The trading price of our shares of common stock could decline due to any of these risks, and you may lose all or part of your investment.

DISCLOSURE REGARDING FORWARD-LOOKING STATEMENTS

This prospectus and the documents that we incorporate herein by reference may contain forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended, or the Securities Act, and Section 21E15(d) of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), incorporated by reference herein, before making an investment decision. Additional risk factors may be included in any prospectus supplements relating to securities described in this prospectus. The occurrence of any of those risks could materially and adversely affect our business, prospects, financial condition, results of operations or the Exchange Act. Forward-looking statements include those that express plans, anticipation, intent, contingency, goals, targets or future development and/or otherwise are not statements of historical fact. Any forward-looking statements are based on our current expectations and projections about future events and are subject tocash flow. Other risks and uncertainties knownthat we do not now consider to be material or of which we are not now aware may become important factors that affect us in the future and unknowncould result in a complete loss of your investment.

DISCLOSURE REGARDING FORWARD-LOOKING STATEMENTS

This prospectus, any prospectus supplement and the documents that could cause actual resultswe incorporate herein or therein by reference contain forward-looking statements, as defined in the Private Securities Litigation Reform Act of 1995.  These statements involve a number of risks and developmentsuncertainties that are difficult to differ materially from those expressed or implied in such statements.

predict.  In some cases, you can identify forward-looking statements by terminology,words such as “may,” “expects,” “intends,” “anticipates,” “intends,“believes,” “estimates,” “plans,” “believes,” “seeks,” “may,“could,” “should,” “could” or the negative of such terms“continue,” “will,” “potential,” “projects” or other similar expressions.  Accordingly,Readers are cautioned that these forward-looking statements speak only as of the date on which the document in which they appear is filed with the SEC, and we do not assume any obligation to update, amend or clarify them to reflect events, new information or circumstances after such dates. Forward-looking statements are subject to risks, uncertainties and assumptions that are difficult to predict. 

Examples of forward-looking statements regarding our business include the following:

These statements involve estimates, assumptions and uncertainties that could cause actual results to differ materially from those expressed in them. Any forward-looking statements are qualified in their entirety by reference to the risk factors described in any accompanying prospectus supplement or in any document incorporated by reference into this prospectus. These factors include, among others:

You should read this prospectus, any accompanying prospectus supplement, any related free writing prospectus and the documents that we reference herein and therein and have filed as exhibits to the registration statement, of which this prospectus is part, completely and with the understanding that our actual future results may be materially different from what we currently expect.  You should assume that the information appearing in this prospectus, any accompanying prospectus supplement, any related free writing prospectus and any document incorporated herein by reference is accurate as of its date only. Because the risk factors referred to above could cause actual results or outcomes to differ materially from those expressed in any forward-looking statements made by us or on our behalf, you should not placeput undue reliance on any forward-looking statements. Further, any forward-looking statement speaks only as of the date on whichstatement.  We believe it is made, andimportant to communicate our expectations to our investors. However, there may be events in the future that we undertake no obligationare not able to update any forward-looking statement to reflect eventsaccurately predict or circumstances after the date on which the statement is made or to reflect the occurrence of unanticipated events. New factors emerge from time to time, and it isthat we do not possible for us to predict which factors will arise. In addition, we cannot assess the impact of each factor on our business or the extent to which any factor, or combination of factors, mayfully control that could cause actual results to differ materially from those containedexpressed or implied in anyour forward-looking statements. We qualify all of

USE OF PROCEEDS

Unless otherwise indicated in the information presented in this prospectus, any accompanying prospectus supplement, any related free writing prospectus and any document incorporated herein by reference, and particularly our forward-looking statements, by these cautionary statements.

USE OF PROCEEDS

Allwe will use the net proceeds from the sale of our common stock coveredsecurities offered by this prospectus is being soldfor general corporate purposes, including working capital, for further research and development and ongoing sales and marketing expenses, and, potentially, capital expenditures and licensing of additional technologies. We may also use a portion of the net proceeds from this offering to acquire or invest in complimentary businesses, technologies, product candidates or other intellectual property, although we have no present commitments or agreements to do so. The timing and amount of our actual expenditures will be based on many factors, including cash flows from operations and the anticipated growth of our business. As a result, unless otherwise indicated in the prospectus supplement, our management will have broad discretion to allocate the net proceeds of the offerings. Pending their ultimate use, we intend to invest the net proceeds in short-term, investment-grade, interest-bearing instruments.

We will not receive any proceeds from sales of warrant shares by orthe selling warrant holder.  Such proceeds would be solely for the account of the selling stockholders. We will receive no proceeds from the sale from time to time of our common stock by the selling stockholders. However, this prospectus covers the offer of shares of common stock issuable in the future upon the exercise of warrants to purchase up to an aggregate of 12,500,000 shares of our common stock, as described below under the heading “Selling Stockholders” in this prospectus, at an exercise price of $1.46 per share. If all of the warrants are exercised in full, we would receive aggregate gross proceeds of approximately $18.25 million. There can be no assurance any of the warrants will be exercised by the selling stockholders. We expect to use proceeds, if any, from exercise of the warrants for funding operations or for working capital or other general corporate purposes, and for any other corporate purposes that we may specify in any prospectus supplement.

We cannot assure that any selling stockholder will sell any or all of the shares of common stock registered pursuant to the registration statement of which this prospectus is a part.warrant holder. The selling security holderswarrant holder will pay any underwriting discounts and commissions and expenses it incurs for brokerage, commissionsaccounting, tax or similar charges incurred forlegal services or any other expenses it incurs in disposing of the sale of such shares of our common stock.warrant shares. We will bear all other costs, fees and expenses incurred in effecting the registration of the warrant shares of common stock covered by this prospectus.

PLAN OF DISTRIBUTION FOR SECURITIES OFFERED BY US

We may sell the securities offered through this prospectus in one or more of the following ways (or in any combination) from time to time:

If underwriters or dealers are used in the sale, the securities will be acquired by the underwriters or dealers for their own account and may be resold from time to time in one or more transactions, including:

The prospectus supplement will include the following information:

Sale Through Underwriters or Dealers

If underwriters are used in the sale of any securities, the underwriters will acquire the securities for their own account, including through underwriting, purchase, security lending or repurchase agreements with us. The underwriters may resell the securities from time to time in one or more transactions, including negotiated transactions. Underwriters may sell the securities in order to facilitate transactions in any of our other securities (described in this prospectus or otherwise), including other public or private transactions and short sales. Underwriters may offer securities to the public either through underwriting syndicates represented by one or more managing underwriters or directly by one or more firms acting as underwriters. Unless otherwise indicated in the prospectus supplement, the obligations of the underwriters to purchase the securities will be subject to certain conditions, and the underwriters will be obligated to purchase all the offered securities if they purchase any of them. The underwriters may change from time to time any initial public offering price and any discounts or concessions allowed or reallowed or paid to dealers. The prospectus supplement will include the names of the principal underwriters, the respective amount of securities underwritten, the nature of the obligation of the underwriters to take the securities and the nature of any material relationship between an underwriter and us.

If dealers are used in the sale of securities offered through this prospectus, we will sell the securities to them as principals. They may then resell those securities to the public at varying prices determined by the dealers at the time of resale. The prospectus supplement will include the names of the dealers and the terms of the transaction.

We may authorize underwriters, dealers or agents to solicit offers by certain purchasers to purchase our securities from us at the public offering price set forth in the prospectus supplement pursuant to delayed delivery contracts providing for payment and delivery on a specified date in the future. The contracts will be subject to those conditions set forth in the prospectus supplement, and the prospectus supplement will set forth any commissions paid for solicitation of these contracts.

Underwriters, dealers and agents may contract for or otherwise be entitled to indemnification by us against certain civil liabilities, including liabilities under the Securities Act, or to contribution with respect to payments made by the underwriters, dealers or agents, under agreements between us on one hand, and the underwriters, dealers and agents, on the other hand.

We may grant underwriters who participate in the distribution of our securities an option to purchase additional securities to cover over-allotments, if any, in connection with the distribution.

Underwriters, dealers, or agents may receive compensation in the form of discounts, concessions or commissions from us or our purchasers, as their agents in connection with the sale of our securities. These underwriters, dealers or agents may be considered to be underwriters under the Securities Act. As a result, discounts, commissions or profits on resale received by the underwriters, dealers or agents may be treated as underwriting discounts and commissions. The prospectus supplement for any securities offered by us will identify any such underwriter, dealer or agent and describe any compensation received by them from us. Any public offering price and any discounts or concessions allowed or re-allowed or paid to dealers may be changed from time to time.

Underwriters, broker-dealers or agents who may become involved in the sale of our securities may engage in transactions with and perform other services for us for which they receive compensation.

Direct Sales and Sales Through Agents

We may sell the securities offered through this prospectus directly. In this case, no underwriters or agents would be involved. Such securities may also be sold through agents designated from time to time. The prospectus supplement will name any agent involved in the offer or sale of the offered securities and will describe any commissions payable to the agent by us. Unless otherwise indicated in the prospectus supplement, any agent will agree to use its reasonable best efforts to solicit purchases for the period of its appointment.

We may sell the securities directly to institutional investors or others who may be deemed to be underwriters within the meaning of the Securities Act, with respect to any sale of those securities.

At-the-Market Offerings

To the extent that we make sales through one or more underwriters or agents in at-the-market offerings, we will do so pursuant to the terms of a sales agency financing agreement or other at-the-market offering arrangement between us, on one hand, and the underwriters or agents, on the other. If we engage in at-the-market sales pursuant to any such agreement, we will issue and sell our securities through one or more underwriters or agents, which may act on an agency basis or a principal basis. During the term of any such agreement, we may sell securities on a daily basis in exchange transactions or otherwise as we agree with the underwriters or agents. Any such agreement will provide that any securities sold will be sold at prices related to the then prevailing market prices for our securities. Therefore, exact figures regarding proceeds that will be raised or commissions to be paid cannot be determined at this time. Pursuant to the terms of the agreement, we may agree to sell, and the relevant underwriters or agents may agree to solicit offers to purchase blocks of our common stock or other securities. The terms of any such agreement will be set forth in more detail in the prospectus supplement.

Market Making, Stabilization and Other Transactions

In connection with an offering through underwriters, an underwriter may, to the extent permitted by applicable rules and regulations, purchase and sell securities in the open market. These transactions, to the extent permitted by applicable rules and regulations, may include short sales, stabilizing transactions and purchases to cover positions created by short sales. Short sales involve the sale by the underwriters of a greater number of securities than they are required to purchase in the offering. “Covered” short sales are short sales made in an amount not greater than the underwriters’ option to purchase additional securities from us in the offering, if any. If the underwriters have an over-allotment option to purchase additional securities from us, the underwriters may consider, among other things, the price of securities available for purchase in the open market as compared to the price at which they may purchase securities through the over-allotment option. “Naked” short sales, which may be prohibited or restricted by applicable rules and regulations, are any sales in excess of such option or where the underwriters do not have an over-allotment option. The underwriters must close out any naked short position by purchasing securities in the open market. A naked short position is more likely to be created if the underwriters are concerned that there may be downward pressure on the price of the securities in the open market after pricing that could adversely affect investors who purchase in the offering.

Accordingly, to cover these short positions or to otherwise stabilize or maintain the price of the securities, the underwriters may bid for or purchase securities in the open market and may impose penalty bids. If penalty bids are imposed, selling concessions allowed to syndicate members or other broker-dealers participating in the offering are reclaimed if securities previously distributed in the offering are repurchased, whether in connection with stabilization transactions or otherwise. The effect of these transactions may be to stabilize or maintain the market price of the securities at a level above that which might otherwise prevail in the open market. The imposition of a penalty bid may also affect the price of the securities to the extent that it discourages resale of the securities. The magnitude or effect of any stabilization or other transactions is uncertain.

Derivative Transactions and Hedging

We, the underwriters or other agents may engage in derivative transactions involving the securities. These derivatives may consist of short sale transactions and other hedging activities. The underwriters or agents may acquire a long or short position in the securities, hold or resell securities acquired and purchase options or futures on the securities and other derivative instruments with returns linked to or related to changes in the price of the securities. In order to facilitate these derivative transactions, we may enter into security lending or repurchase agreements with the underwriters or agents. The underwriters or agents may effect the derivative transactions through sales of the securities to the public, including short sales, or by lending the securities in order to facilitate short sale transactions by others. The underwriters or agents may also use the securities purchased or borrowed from us or others (or, in the case of derivatives, securities received from us in settlement of those derivatives) to directly or indirectly settle sales of the securities or close out any related open borrowings of the securities.

Trading Market and Listing of Securities

Any common stock sold or resold pursuant to a prospectus supplement will be listed on The NASDAQ Capital Market or on such other national securities exchange as our common stock may then be listed. The securities other than common stock may or may not be listed on a national securities exchange. It is possible that one or more underwriters may make a market in a class or series of securities, but the underwriters will not be obligated to do so and may discontinue any market making at any time without limitation, all registrationnotice. We cannot give any assurance as to the liquidity of the trading market for any of the securities. 

General Information

Agents, underwriters, and filing fees, printing feesdealers may be entitled, under agreements entered into with us, to indemnification by us against certain liabilities, including liabilities under the Securities Act.

SELLING WARRANT HOLDER

This prospectus also relates to the possible offering and fees and expensessale, from time to time, of up to 70,000 warrant shares by the selling warrant holder, subject to anti-dilution adjustment. The selling warrant holder does not own any of our counsel and accountants.

SELLING STOCKHOLDERS

Thesecurities other than the warrant shares registered under the registration statement of which this prospectus forms a part. We issued four warrants exercisable for shares of our common stock to which this prospectus relates are being registered for salethe selling warrant holder pursuant to a financial public investor relations agreement, dated as of November 1, 2011, as amended, between us and the selling warrant holder.  In July 2014, we terminated that agreement with the selling warrant holder. The terms of the warrants held by the selling stockholders named below. We have registered the shares to permitwarrant holder are described under “Description of Capital Stock – Warrants – Outstanding Warrants.” Additional information about the selling stockholders and certain of their transferees afterwarrant holder may be set forth in one or more prospectus supplements or in filings that we make with the date of this prospectus to sellSEC under the shares when they deem appropriate. We refer to all of these possible sellers as the “selling stockholders”Exchange Act that are incorporated by reference in this prospectus. 

The selling stockholders may sell all, a portion or nonefollowing table sets forth information regarding beneficial ownership of their shares at any time.

On May 8, 2013, we entered into a Purchase Agreement with the selling stockholders pursuant to which Vermillion sold a total of 8,000,000 shares of common stock, priced at $1.46 per share, for an aggregate purchase price of $11,680,000. The selling stockholders also received warrants to purchase up to 12,500,000 shares of common stock at an exercise price of $1.46 per share for a purchase price of $0.125 for each share of common stock subject to such warrants. The warrants are exercisable for 3 years beginning ninety days following the date of issuance. The shares ofour common stock and the warrants (includingby the shares issuable upon exerciseselling warrant holder as of September 22, 2014.

(1)Also includes any sale of the warrants) were issued in a private placement, subject to customary registration rights under a stockholders agreement among Vermillionwarrants and the underlying warrant shares by pledges, donees, transferees or other successors in interest that receive such securities by pledge, gift, distribution or other non-sale related transfer from the selling stockholders (the “Stockholders Agreement”). Underwarrant holder after the Stockholders Agreement, Vermillion agreed to file aeffective date of the registration statement of which this prospectus isforms a part with the SEC to register the sale bypart. The information concerning the selling stockholderswarrant holder may change from time to time, and any changes and the names of any transferees, pledges, donees, and other successors in interest will be set forth in supplements to this prospectus to the extent required.

(2)The number of shares of our common stock indicated assumes exercise of all of the 8,000,000 sharesselling warrant holder’s warrants, each for one share of common stock issuedand a cash payment in lieu of the private placement, together withissuance of any fractional share interest. However, the 12,500,000number of shares of common stock that may be issuedissuable upon exercise of the warrants. The securities were sold pursuant to the exemption from registration under Rule 506 promulgated under the Securities Act.

Under the terms of the Stockholders Agreement, if at any time Vermillion makes certain offerings of shares of common stock or common stock equivalents (or a combination of units thereof) for cash,warrant is subject to certain exceptions, certain selling stockholders will haveanti-dilution protections as described under “Description of Capital Stock – Warrants – Outstanding Warrants.” As a result, the right to participate in such financing on the same terms, conditions and price provided for in such financing, subject to the terms and conditions of the Stockholders Agreement.

The foregoing description is qualified in its entirety by the complete provisions of the Purchase Agreement and the Stockholders Agreement, which are attached as exhibits to the Form 8-K (File No. 001-34810) which was filed by us with the Securities and Exchange Commission on May 14, 2013 and is incorporated herein by reference.

The following table sets forth the maximum number of shares of common stock to be sold by the selling stockholders. The percentage of shares beneficially owned after the offering is based on 23,486,261 shares of our common stock outstanding as of June 30, 2013. Except as otherwise indicated, each selling stockholder has sole voting and dispositive power with respect to such shares. We have prepared this table using information furnished to us by or on behalfissuable upon exercise of the selling stockholders.warrants may increase or decrease in the future.

*Less than 1%.

(2)

Assumes that the selling stockholders dispose of all of the shares of common stock covered by this prospectus and do not acquire beneficial ownership of any additional shares. The registration of these shares does not necessarily mean that the selling stockholders will sell all or any portion of the shares covered by this prospectus.

(3)

Oracle Investment Management, Inc. (“Oracle Manager”) is the investment manager to Oracle Ten Fund Master, LP (“Oracle Ten Fund”), Oracle Associates, LLC (“Oracle Associates”) is the general partner of Oracle Partners, LP and Oracle Ten Fund and Larry N. Feinberg is the managing member of Oracle Associates and the sole shareholder, director and president of the Oracle Manager. By virtue of these relationships, Oracle Manager may be deemed to have voting and dispositive power over the shares held by Oracle Ten Fund and Oracle Associates and Larry N. Feinberg may be deemed to have voting and dispositive power over the shares of Oracle Ten Fund and Oracle Partners, LP.

(4)

Matthew Strobeck has voting and dispositive power over the shares of common stock and shares of common stock underlying the warrants acquired pursuant to the Purchase Agreement. In addition, Mr. Strobeck may be deemed to have voting and dispositive power over 31,000 shares of common stock held in custodial accounts in the name of his wife for the benefit of his children.

(5)	Adam Usdan, as the sole trustee of the Feinberg Family Trust (“Trust”), may be deemed to have voting and dispositive power over the shares of common stock held by the Trust.

(6)

Includes warrants to purchase shares of common stock as follows: Jack W. Shuler 4,055,157; Oracle Partners, LP 2,761,990; Oracle Ten Fund Master, LP 1,577,990; Matthew Strobeck 1,233,543; Feinberg Family Trust 831,000; Tino Hans Shuler Trust 517,349; Tanya Eve Shuler Trust 517,349; Therese Heidi Shuler Trust 517,349; John Patience 267,551; The Seamark Fund, L.P. 103,000; Michael Gordon 74,914; and Lawrence Mehren 42,808

PLAN OF DISTRIBUTION

We are registering 20,500,000 shares of our common stock on behalf of the selling stockholders. FOR WARRANT SHARES OFFERED BY THE SELLING WARRANT HOLDER

The selling stockholderswarrant holder may from time to time, offer and sell all or a portion of the warrant shares covered by this prospectus from time to time, in one or more or any combination of the following transactions:

The selling stockholderswarrant holder may sell the shares at prices then prevailing or related to the then current market price or at negotiated prices. The offering price of the shares from time to time will be determined by the selling stockholderswarrant holder and, at the time of the determination, may be higher or lower than the market price of our common stock on the NasdaqThe NASDAQ Capital Market or any other exchange or market.

The shares may be sold directly or through broker-dealers acting as principal or agent, or pursuant to a distribution by one or more underwriters on a firm commitment or best-efforts basis. In connection with an underwritten offering, underwriters or agents may receive compensation in the form of discounts, concessions or commissions from the selling stockholderswarrant holder or from purchasers of the offered warrant shares for whom they may act as agents. In addition, underwriters may sell the warrant shares to or through dealers, and those dealers may receive compensation in the form of discounts, concessions or commissions from the underwriters and/or commissions from the purchasers for whom they may act as agents. In connection with any particular offering pursuant to this shelf registration statement,of warrant shares, an underwriter may engage in stabilizing transactions, short sales, syndicate covering transactions and penalty bids. The selling stockholderswarrant holder and any underwriters, dealers or agents participating in a distribution of the shares may be deemed to be “underwriters” within the meaning of the Securities Act, and any profit on the sale of the shares by the selling stockholderswarrant holder and any commissions received by broker-dealers may be deemed to be underwriting commissions under the Securities Act. Broker-dealers may receive commissions or discounts from the selling stockholderswarrant holder (or, if any broker-dealer acts as agent for the purchaser of shares, from the purchaser) in amounts to be negotiated, but, except as set forth in a supplement to this prospectus, in the case of an agency transaction not in excess of a customary brokerage commission in compliance with NASD Rule 2440 of the Financial Industry Regulatory Authority (“FINRA”FINRA”); and in the case of a principal transaction a markup or markdown in compliance with FINRA’s NASD IM-2440.

In connection with the sale of the warrant shares, of our common stock or interests therein, the selling stockholderswarrant holder may enter into hedging transactions with broker-dealers or other financial institutions, which may in turn engage in short sales of the warrant shares of our common stock in the course of hedging the positions they assume. The selling stockholderswarrant holder may also sell warrant shares of our common stock short and deliver these securities to close out their short positions, or loan or pledge the common stockwarrant shares to broker-dealers that in turn

may sell these securities. The selling stockholderswarrant holder may also enter into option or other transactions with broker-dealers or other financial institutions for the creation of one or more derivative securities which require the delivery to such broker-dealer or other financial institution of warrant shares, offered by this prospectus, which warrant shares such broker-dealer or other financial institution may resell pursuant to this prospectus (as supplemented or amended to reflect such transaction).

We and the

The selling stockholderswarrant holder may agree to indemnify an underwriter, broker-dealer or agent against certain liabilities related to the selling of the common stock, including liabilities arising under the Securities Act. In connection with the private placement we have also agreed to pay the costs, expenses and fees of registering the shares of common stock, and agreed to indemnify the selling stockholders against liabilities, including under the Securities Act, relating to registration of shares offered by this prospectus. We will not be responsible for any underwriting discounts or commissions associated with the sale of such shares.

We are not aware that anythe selling stockholders havewarrant holder has entered into any agreements, understandings or arrangements with any underwriters or broker-dealers regarding the sale of their shares. Upon our notification by the selling stockholderswarrant holder that any material arrangement has been entered into with an underwriter or broker-dealer for the sale of shares through a block trade, special offering, exchange distribution, secondary distribution or a purchase by an underwriter or broker-dealer, we will file a supplement to this prospectus, if required, pursuant to Rule 424(b) under the Securities Act, disclosing certain material information, including:

The selling stockholders arewarrant holder is subject to the applicable provisions of the Exchange Act and the rules and regulations under the Exchange Act, including Regulation M. This regulation may limit the timing of purchases and sales of any of the warrant shares of common stock offered in this prospectus by the selling stockholders.warrant holder. The anti-manipulation rules under the Exchange Act may apply to sales of warrant shares in the market and to the activities of the selling stockholderswarrant holder and theirits affiliates. Furthermore, Regulation M may restrict the ability of any person engaged in the distribution of the warrant shares to engage in market-making activities for the particular securities being distributed for a period of up to five business days before the distribution. The restrictions may affect the marketability of the warrant shares and the ability of any person or entity to engage in market-making activities for the warrant shares.

To the extent required, this prospectus may be amended and/or supplemented from time to time to describe a specific plan of distribution. The selling stockholderswarrant holder may sell the shares of common stock in compliance with the provisions of Rule 144 under the Securities Act, if available, or pursuant to other available exemptions from the registration requirements of the Securities Act.

The warrant shares registered hereunder will be sold only through registered or licensed brokers or dealers if required under applicable state securities laws. In addition, in certain states, such shares may not be sold unless they have been registered or qualified for sale in the applicable state or an exemption from the registration or qualification requirement is available and is complied with.

DESCRIPTION OF CAPITAL STOCK

Authorized and Outstanding Capital Stock

Under our amended and restated certificate of incorporation, our authorized capital stock consists of 150,000,000 shares of common stock, par value $0.001 per share and 5,000,000 shares of preferred stock, par value $0.001 per share. As of June 30, 2013, there were approximately 23,486,261 shares of common stock outstanding, 745,468 shares of common stock reserved for issuance upon exercise of outstanding stock options, 12,584,000 shares of common stock reserved for issuance upon exercise of outstanding warrants to purchase common stock, and no shares of preferred stock outstanding.

The following summary description of our capital stock is based on the applicable provisions of the Delaware General Corporation Law, or DGCL, and on the provisions of our certificateFourth Amended and Restated Certificate of incorporation,Incorporation, dated January 22, 2010, as amended effective June 19, 2014 (our “Certificate of Incorporation”), and our bylaws, as amended.Fifth Amended and Restated Bylaws, effective June 19, 2014 (our “Bylaws”). This information is qualified entirely by reference to the applicable provisions of the Delaware General Corporation LawDGCL, our Certificate of Incorporation, and our certificate of incorporation, as amended, and our bylaws, as amended.Bylaws. For information on how to obtain copies of such documents,our Certificate of Incorporation and our Bylaws, please refer to the heading “Where You Can Find More Information” in this prospectus.

CommonOur Authorized Capital Stock

Under our Certificate of Incorporation, our authorized capital stock consists of 150,000,000 shares of common stock, par value $0.001 per share, and 5,000,000 shares of preferred stock, par value $0.001 per share. 

Common Stock

As of JuneSeptember 30, 2013,2014, we had 23,486,26135,962,514 shares of our common stock outstanding, 1,944,747 shares of our common stock that were subject to outstanding options, 23,750 shares of our common stock subject to existing restricted stock grants and 77,379763,838 shares of our common stock reserved for future issuance to employees, directors and consultants pursuant to our employee stock plans, which excludes 745,468 shares of our common stock that were subject to outstanding options and 5,000 shares of our common stock subject to existing restricted stock grants.incentive plans. In addition, as of JuneSeptember 30, 2013,2014, warrants to purchase 12,584,000483,359 shares of our common stock were outstanding at exercise prices ranging from $1.46 to $3.23$4.70 per share, with a weighted average exercise price of $1.47$1.65 per share.

In addition, our Board  All outstanding shares of Directors has approved grantscommon stock are, and the shares of an additional 642,500common stock options to officersoffered by us in this offering, when issued and employees whichpaid for will be, fully paid and nonassessable. The rights, preferences and privileges of the holders of common stock are subject to, and may be adversely affected by, the approval by our stockholdersrights of an increasethe holders of shares of any series of preferred stock which we may designate in the number of shares authorized under our 2010 Stock Incentive Plan.future.

Voting Rights

Each holder of common stock is entitled to one vote for each share on all matters to be voted upon by the stockholders, and there are no cumulative voting rights.

Dividend Rights

Subject to preferences to which holders of preferred stock may be entitled and the rights of certain of our stockholders set forth in the Stockholders Agreement (as defined below), holders of common stock are entitled to receive ratably such dividends, if any, as may be declared from time to time by theour Board of Directors out of funds legally available therefor. We have never paid or declared any dividend on our common stock, and we do not anticipate paying cash dividends on any common stock in the foreseeable future.  We intend to retain all available funds and any future earnings to fund the development and expansion of our business.

No Preemptive or Similar Rights

Holders of our common stock do not have preemptive rights, and our common stock is not convertible or redeemable.  As described under “Stockholders Agreement,” certain holders of our common stock have the right to purchase shares in connection with most equity offerings made by the Company.

Right to Receive Liquidation Distributions

In the event of aour liquidation, dissolution or winding up, of us, holders of common stock would be entitled to share in our assets remaining after the payment of liabilities and the satisfaction of any liquidation preference granted the holders of any outstanding shares of preferred stock. Holdersany senior class of common stock have no preemptive or conversion rights or other subscription rights and there are no redemption or sinking fund provisions applicable to the common stock. All outstanding shares of common stock are, and the shares of common stock offered by us in this offering, when issued and paid for will be, fully paid and nonassesable.securities. The rights, preferences and privileges of the holders of common stock are subject to, and may be adversely affected by, the rights of the holders of shares of any series of preferred stock which we may designate in the future.

Preferred Stock

There are no shares of our preferred stock outstanding.

Our Board of Directors is authorized, subject to any limitations prescribed by law, without stockholder approval, to issue from time to time up to an aggregate of 5,000,000 shares of preferred stock, in one or more series, each of such series to have such rights and preferences, including voting rights, dividend rights, conversion rights, redemption privilegesterms and liquidation preferences as shall be determined by theour Board of Directors. The rights forAny issuance of shares of preferred stock could adversely affect the voting power of holders of

common stock, and the likelihood that the holders of commonpreferred stock will be subject to,receive dividend payments and may be adversely affected by, the rights of holders of any preferred stock that may be issued in the future. Issuance of preferred stock, while providing desirable flexibility in connection with possible acquisitions and other corporate purposes,payments upon liquidation could have the effect of making it more difficult fordelaying, deferring or preventing a third party to acquire, or of discouraging a third party from attempting to acquire, a majority of the outstanding voting stock of us. We have no present plans to issue any shares of preferred stock.change in control.

Warrants

Outstanding Warrants

As of JuneSeptember 30, 2013,2014, warrants to purchase 12,584,000483,359 shares of common stock at exercise prices ranging from $1.46 to $3.23$4.70 were outstanding, with a weighted exercise price of $1.47$1.65 per share. All outstanding warrants contain provisions for the adjustment of the exercise price in the event of stock dividends, stock splits, reorganizations, reclassifications or mergers. In addition, 84,000 of the warrants contain a “cashless exercise” feature that allows the holders thereof to exercise the warrants without a cash payment to us under certain circumstances. The rights of the shares of common stock issuable upon exercise of all of our outstanding warrants shall beare the same as those described under “Common Stock” above.

Pursuant to a financial public investor relations agreement, dated as of November 1, 2011, as amended, between us and the selling warrant holder, we issued four warrants for an aggregate of 70,000 shares of our common stock to the selling warrant holder. If the selling warrant holder does not sell all of its 70,000 warrant shares under this registration statement, it will have  “piggyback” registration rights with respect to the remaining warrant shares for any additional registration statements that we file on our own account or the account of others with respect to shares of our common stock. The following table sets forth the date of issuance, expiration date, number of shares of underlying common stock and initial exercise price associated with each warrant held by the selling warrant holder.

(1)The warrant dated May 1, 2014 was initially exercisable for 21,000 shares of our common stock, but, in accordance with its terms, did not fully vest due to the termination of our agreement with the selling warrant holder in July 2014.

The foregoing description of our outstanding warrants is qualified entirely by reference to exhibits 4.5, 4.6, 4.7 and 4.8 to the registration statement of which this prospectus forms a part.

Warrants Registered by Us Hereunder

We may issue warrants to purchase shares of common stock or shares of preferred stock, independently or together with other securities. Warrants sold with other securities may be attached to or separate from the other securities. We will issue warrants under one or more warrant agreements between us and a warrant agent we will name in the prospectus supplement.

The prospectus supplement relating to any warrants we are offering will include specific terms relating to the offering. These terms will include some or all of the following:

Rights

We may issue rights for the purchase of shares of our common stock or shares of our preferred stock. Each series of rights will be issued under a separate rights agreement which we will enter into with a bank or trust company, as rights agent, all as set forth in the applicable prospectus supplement. The rights agent will act solely as our agent in connection with the certificates relating to the rights and will not assume any obligation or relationship of agency or trust with any holders of rights certificates or beneficial owners of rights. We will file the rights agreement and the rights certificates relating to each series of rights with the SEC and incorporate them by reference as an exhibit to the registration statement of which this prospectus is a part on or before the time we issue a series of rights.

The applicable prospectus supplement will describe the terms of any rights we issue, including as applicable:

Rights will be exercisable for U.S. dollars only and will be in registered form only.

Units

We may issue securities in units, each consisting of two or more types of securities. For example, we might issue units consisting of a combination of common stock and warrants to purchase common stock. If we issue units, the prospectus supplement relating to the units will contain the information described above with regard to each of the securities that is a component of the units. In addition, the prospectus supplement relating to the units will describe the terms of any units we issue, including as applicable:

Stockholders Agreement

In connection with a private placement in May 2013, we entered into a stockholders agreement with the purchasers named in that agreement. Pursuant to and subject to the terms of the stockholders agreement, certain of the investors received rights to participate in any future equity offerings on the same price and terms as other investors, and rights to exercise “piggyback” registration rights for any registration statements that we file prior to May 13, 2018 on our own account or for the account of others with respect to shares of our common stock. Some or all of such investors might participate in one or more of the equity offering under the registration statement of which this prospectus is a part.

In addition, the stockholders agreement prohibits the company from taking material actions without the consent of at least one of the two primary investors. These material actions include:

•  making any acquisition with value greater than $2 million;

•  entering into, or amending the terms of agreements with Quest Diagnostics Incorporated, provided that such investors’ consent shall not be unreasonably withheld, conditioned or delayed following good faith consultation with the company;

•  submitting any resolution at a meeting of stockholders or in any other manner changing or authorizing a change in the size of our Board of Directors;

•  offering, selling or issuing any securities senior to our common stock or any securities that are convertible into or exchangeable or exercisable for securities ranking senior to our common stock;

•  amending our Certificate of Incorporation or our Bylaws in any manner that affects the rights, privileges or economics of our common stock or the warrants purchased in the May 2013 private placement;

•  taking any action that would result in a change in control of Vermillion or an insolvency event;

•  paying or declaring dividends on any securities of the company or distributing any assets of the company other than in the ordinary course of business or repurchasing any outstanding securities of the company; or

•  adopting or amending any shareholder rights plan.

In addition, the two primary investors each received the right to designate a person to serve on our Board of Directors. These rights terminate for each stockholder when that stockholder ceases to beneficially own less than 50% of the shares and warrants (taking into account shares issued upon exercise of the warrants), in the aggregate, than were purchased at the closing of the private placement.

Section 203 of the Delaware Corporation Law

We are subject to Section 203 of the General Corporation Law of the State of Delaware, or DGCL, which prevents an “interested stockholder” (defined in Section 203 of the DGCL, generally, as a person owning 15% or more of a corporation’s outstanding voting stock), from engaging in a “business combination” (as defined in Section 203 of the DGCL) with a publicly-held Delaware corporation for three years following the date such person became an interested stockholder, unless:

The provisions of Section 203 of the DGCL could make a takeover of our company difficult.

Effect of Certain Provisions of ourOur Certificate of Incorporation and Bylaws

Certain provisions of our Certificate of Incorporation and Bylaws may have the effect of making it more difficult for a third party to acquire, or of discouraging a third party from attempting to acquire, control of us. Such provisions could limit the price that certain investors might be willing to pay in the future for sharesour securities. Our Certificate of our common stock. Our Bylaws eliminateIncorporation eliminates the right of stockholders to call special meetings of stockholders or to act by written consent without a meeting, and our Bylaws require advance notice for stockholder proposals and director nominations, which may preclude stockholders from bringing matters before an annual meeting of stockholders or from making nominations for directors at an annual meeting of stockholders. The amendmentOur Certificate of any of the foregoing provisions of our Bylaws would require approval by the Board of Directors or the holders of at least 66 2/3% of our outstanding common stock. The authorization ofIncorporation authorizes undesignated preferred stock, which makes it possible for theour Board of Directors to issue preferred stock with voting or other rights or preferences that could impede the success of any attempt to change control of us.

These and other provisions may have the effect of deferring hostile takeovers or delaying changes in control or management of us. The amendment of any of thesethe provisions inof our Certificate of Incorporation described in the immediately preceding paragraph would require approval by theour Board of Directors and the holdersaffirmative vote of at least 66 2/3% of our then outstanding common stock.voting securities, and the amendment of any of the provisions of our Bylaws described in the immediately preceding paragraph would require approval by our Board of Directors or the affirmative vote of at least 66 2/3% of our then outstanding voting securities.

Transfer Agent

The transfer agent for our common stock is Wells Fargo Shareowner Services.

Listing

Our common stock is listed on theThe NASDAQ Capital Market under the symbol “VRML.”

LEGAL MATTERS

Paul HastingsSidley Austin LLP will passhas passed upon the validity of the shares of common stocksecurities being registered by the registration statement of which this prospectus is a part.

EXPERTS Additional legal matters may be passed upon for us or any underwriters, dealers or agents, by counsel that we will name in the applicable prospectus supplement. 

EXPERTS

The consolidated financial statements as of December 31, 2013 and 2012 and for the yearyears then ended incorporated by reference in this Prospectusprospectus have been so incorporated in reliance on the report of BDO USA, LLP, an independent registered public accounting firm, (the report on the financial statements contains an explanatory paragraph regarding the Company’s ability to continue as a going concern), incorporated herein by reference, given on the authority of said firm as experts in auditing and accounting.

The consolidated financial statements for the year ended December 31, 2011 incorporated in this Prospectus by reference to the Annual Report on Form 10-K for the year ended December 31, 2012 have been so incorporated in reliance on the report of PricewaterhouseCoopers LLP, an independent registered public accounting firm, given on the authority of said firm as experts in auditing and accounting.

MATERIAL CHANGES

None

WHERE YOU CAN FIND MORE INFORMATION

We are a reporting company and file annual, quarterly and current reports, proxy statements and other information with the SEC. We have filed with the SEC a registration statement on Form S-3 under the Securities Act with respect to the common stocksecurities we are offering under this prospectus. This prospectus does not contain all of the information set forth in the registration statement and the exhibits to the registration statement. For further information with respect to us and the shares of common stocksecurities we are offering under this prospectus, we refer you to the registration statement and the exhibits and schedules filed as a part of the registration statement. You may read and copy the registration statement, as well as our reports, proxy statements and other information, at the SEC’s Public Reference Room at 100 F Street, N.E., Washington, D.C. 20549. Please call the SEC at 1-800-SEC-0330 for more information about the operation of the Public Reference Room. The SEC maintains an Internet site that contains reports, proxy and information statements, and other information regarding issuers that file electronically with the SEC, including Vermillion, Inc. The SEC’s Internet site can be found athttp://www.sec.gov.

Information on any Vermillion website, any subsection, page, or other subdivision of any Vermillion website, or any website linked to by content on any Vermillion website, is not part of this prospectus and you should not rely on that information unless that information is also in this prospectus or incorporated by reference in this prospectus.

DISCLOSURE OF COMMISSION POSITION ON INDEMNIFICATION FOR SECURITIES ACT LIABILITIES

Insofar as indemnification for liabilities arising under the Securities Act may be permitted to our directors, officers, and persons controlling us pursuant to the provisions described in Item 15 of the registration statement of which this prospectus is a part or otherwise, we have been advised that in the opinion of the SEC such indemnification is against public policy as expressed in the Securities Act and is therefore unenforceable. In the event that a claim for indemnification against such liabilities (other than our payment of expenses incurred or paid by our directors, officers, or controlling persons in the successful defense of any action, suit, or proceeding) is asserted by our directors, officers, or controlling persons in connection with the common stock being registered, we will, unless in the opinion of our counsel the matter has been settled by controlling precedent, submit to a court of appropriate jurisdiction the question whether such indemnification by it is against public policy as expressed in the Securities Act and will be governed by the final adjudication of the issue.

IMPORTANT INFORMATION INCORPORATED BY REFERENCE

The SEC allows us to “incorporate by reference” information into this prospectus, which means that we can disclose important information to you by referring you to another document filed separately with the SEC. The documents incorporated by reference into this prospectus contain important information that you should read about us.

The following documents are incorporated by reference into this prospectus: