Exhibit 99.6 BLUE VALLEY BAN CORP SUBSCRIPTION RIGHTS OFFERING THIS SUBSCRIPTION RIGHTS OFFERING EXPIRES AT 5:00 P.M., EASTERN TIME, ON DECEMBER 5, 2008, UNLESS THE EXERCISE PERIOD IS EXTENDED (SUCH DATE AND TIME, AS IT MAY BE EXTENDED, THE "EXPIRATION DATE"). Blue Valley Ban Corp has distributed to each holder of its common stock owned of record at 5:00 p.m., Eastern time on November 10, 2008 (each an "Eligible Holder"), at no charge, one nontransferable right to purchase .1352 shares of common stock of Blue Valley Ban Corp at $18.00 per full share (the "Subscription Rights"). Each Subscription Right entitles an Eligible Holder who fully exercises its basic subscription privilege to subscribe, prior to the Expiration Date, for additional shares of common stock of Blue Valley Ban Corp at an exercise price of $18.00 per full share to the extent that any shares are not purchased by other Eligible Holders under their basic subscription privilege as of the Expiration Date or to the extent the Company decides to increase the size of the offering (the "Oversubscription Privilege"). The terms and conditions of the Subscription Rights offering are set forth in Blue Valley Ban Corp's Prospectus dated November 10, 2008 (as it may be amended or supplemented, the "Prospectus"), which is incorporated into this certificate by reference. Capitalized terms used but not defined herein have the meanings set forth in the Prospectus. The owner of this certificate is entitled to the number of basic Subscription Rights, and is entitled to exercise the basic Subscription Rights for the number of shares, shown on this Rights Certificate. THE DISCOUNT RIGHTS ARE NONTRANSFERABLE The Subscription Rights are nontransferable. The Subscription Rights will not be listed on any securities exchange or quoted on any automated quotation system. Blue Valley Ban Corp cannot assure you that the shares of common stock of Blue Valley Ban Corp issued in respect of exercised Subscription Rights will ever be listed on the New York Stock Exchange, the Nasdaq Global Select Market or any other securities exchange or quotation system. EXERCISE PRICE The exercise price for the Subscription Rights and the Oversubscription Privilege is $18.00 in cash per full share. A fractional Subscription Right will not be exercisable unless it is aggregated with other fractional Subscription Rights so that when exercised, in the aggregate, such fractional Subscription Rights result in the purchase of a whole share of common stock of Blue Valley Ban Corp. In other words, fractional Subscription Rights cannot be exercised for fractional shares of common stock of the Company. METHOD OF EXERCISE OF RIGHTS IN ORDER TO EXERCISE YOUR SUBSCRIPTION RIGHTS, YOU MUST PROPERLY COMPLETE AND SIGN THIS RIGHTS CERTIFICATE ON THE BACK AND RETURN IT IN THE ENVELOPE PROVIDED TO COMPUTERSHARE TRUST COMPANY, N.A., TOGETHER WITH PAYMENT IN FULL FOR AN AMOUNT EQUAL TO THE APPLICABLE EXERCISE PRICE MULTIPLIED BY THE TOTAL NUMBER OF SHARES OF COMMON STOCK THAT YOU ARE REQUESTING TO PURCHASE TO
THE RIGHTS AGENT, COMPUTERSHARE TRUST COMPANY, N.A., BEFORE 5:00 P.M., EASTERN TIME, ON DECEMBER 5, 2008. Holder ID COY Class Rights Qty Issued Rights Cert # 123456789 XXXX Subscription Rights XXX.XXXXXX 12345678 Signature of Owner and U.S. Person for Signature of Co-Owner (if more than Date (mm/dd/yyyy) Tax Certification one registered holder listed) - ---------------------------------------- -------------------------------------- -------------------------------------- - ---------------------------------------- -------------------------------------- -------------------------------------- Full payment of the exercise price for each share of common stock you wish to purchase be must made in U.S. dollars by (1) certified check drawn upon a U.S. bank payable to the rights agent, or (2) cashier's check drawn upon a U.S. bank or express money order payable to the rights agent, in each case in accordance with the "Instructions as to Use of Blue Valley Ban Corp Subscription Rights Certificates" that accompanied the mailing of the Prospectus. Notwithstanding the foregoing, Eligible Holders who hold shares as a depository or nominee must make all payments by wire transfer of immediately available funds to the account maintained by the rights agent. The rights agent will not accept non-certified checks drawn on personal or business accounts. Payments of the exercise price for the common stock will be held in an escrow account until five business days following the Expiration Date, unless Blue Valley Ban Corp withdraws or terminates the Subscription Rights offering. No interest will be paid to you on the funds you deposit with the rights agent. You will not receive any interest on the payments held by the rights agent before your shares have been issued to you or your payment is returned to you, without interest, because your exercise has not been satisfied for any reason. 2
- ---------------------------------------------------------------------------------------------------------------------------------------- PLEASE PRINT ALL INFORMATION CLEARLY AND LEGIBLY - ---------------------------------------------------------------------------------------------------------------------------------------- SECTION 1: OFFERING INSTRUCTIONS (check the appropriate boxes) IF YOU WISH TO SUBSCRIBE FOR YOUR FULL ENTITLEMENT OF SUBSCRIPTION RIGHTS: I apply for ALL of my entitlement _______________ x .1352 = ________________ x 18.00 = $_______________ of new shares pursuant to the basic (no. of subscription rights) (no. of new shares) (per share) subscription Example: If you own 1,000 shares of common stock, your basic subscription right permits the purchase of 135 shares. (1,000 purchase rights/7.396 = 135.21, with fractional shares rounded down to the nearest whole number]. In addition, I apply for additional shares pursuant to the ________________ x 18.00 = $_______________ oversubscription privilege* (no. of new shares) (per share) IF YOU DO NOT WISH TO APPLY FOR YOUR FULL ENTITLEMENT OF SUBSCRIPTION RIGHTS: I apply for ________________ x 18.00 = $_______________ (no. of new shares) (per share) Amount of check or money order enclosed or wire transmitted IF YOU DO NOT WISH TO EXERCISE YOUR RIGHT TO SUBSCRIBE: Please disregard this mailing. - --------------------------------------------------------------------------------------------------------------------------------------- SECTION 2: SUBSCRIPTION AUTHORIZATION: I acknowledge that I have received the Prospectus for this offering of Subscription Rights and I hereby subscribe for the number of shares indicated above on the terms and conditions specified in the Prospectus relating to the primary subscription and the oversubscription privilege in the Subscription Rights offering. Signature of Subscriber(s) - -------------------------------------------------------------------------------- (and address if different than that listed on this Subscription Certificate) - -------------------------------------------------------------------------------- - -------------------------------------------------------------------------------- Telephone number (including area code) -------------------------------- - -------------------------------------------------------------------------------- * You can only participate in the oversubscription privilege if you have subscribed for your full entitlement of new shares pursuant to the basic subscription. Please complete all applicable information and return to: COMPUTERSHARE TRUST COMPANY, N.A. By First Class Mail: Computershare Trust Company, N.A., Corporate Actions Voluntary Offer, P.O. Box 43011, Providence, RI 02940-3011 By Hand, Express Mail or Overnight Delivery: Computershare Trust Company, N.A., Corporate Actions Voluntary Offer, 250 Royall Street, Suite V, Canton, MA 02021 DELIVERY OF THIS SUBSCRIPTION CERTIFICATE TO AN ADDRESS OTHER THAN AS SET FORTH ABOVE DOES NOT CONSTITUTE A VALID DELIVERY Any questions regarding this Subscription Certificate and the Subscription Rights Offering may be directed to Computershare Inc., toll free at (800) 962-4284. 3