<Page>
Exhibit 99.1
Richard Dressler
Vice President, Finance, Chief Financial Officer, and Treasurer
Voice: 860-347-8506
inquire@zygo.com
For Immediate Release
ZYGO ANNOUNCES FISCAL 2004 FIRST QUARTER RESULTS
MIDDLEFIELD, CONNECTICUT (OCTOBER 30, 2003).....Zygo Corporation (NASDAQ: ZIGO)
Net sales of $24.2 million for the first quarter of fiscal 2004 increased by
$3.8 million, or 19%, over the comparable prior year period sales of $20.4
million. Net sales for the first quarter of fiscal 2004 included $4.4 million
from a development services agreement, as compared to $2.7 million in the
comparable prior year period.
For the first quarter of fiscal 2004, net sales in the semiconductor segment
were $12.2 million, or 50% of total net sales, as compared with $10.8 million,
or 53%, in the prior year period, and net sales in the industrial segment were
$12.0 million, or 50% of total net sales, as compared with $9.6 million, or 47%,
in the prior year period. The increase in net sales in the semiconductor segment
was primarily due to an increase in sales in Japan, including an increase of
$1.7 million from the development services agreement, partially offset by a
decrease in sales in Europe. The increase in net sales in the industrial segment
was primarily due to an increase in sales in the Pacific Rim and Japan, offset
slightly by a decrease in sales in Europe.
The Company recorded a net loss of $0.8 million for the first quarter of fiscal
2004 as compared with a net loss of $11.9 million for the first quarter of
fiscal 2003. On a per share basis, the net loss was $0.05 per share for the
first quarter of fiscal 2004 as compared with a net loss of $0.68 per share for
the first quarter of fiscal 2003. The net loss for the first quarter of fiscal
2004 and the net loss for the first quarter of fiscal 2003 include the loss from
discontinued operations of our TeraOptix unit of $0.1 million and $11.0 million,
respectively. The loss from continuing operations was $0.7 million, or $0.04 per
share, for the first quarter of fiscal 2004, as compared with a loss of $0.8
million, or $0.05 per share, for the first quarter of fiscal 2003.
As previously announced, the Company discontinued its telecommunications
TeraOptix business unit. The Company disposed of its equipment and is currently
marketing for sale its facility located in Westborough, Massachusetts.
Accordingly, the results of TeraOptix have been presented as a separate line
item on the statements of operations as discontinued operations, net of
tax, for all periods presented. In addition, the charges on the disposal of the
business, net of
1
<Page>
tax, have been recorded as a line item for the fiscal 2003 period presented.
All continuing operations line items presented exclude TeraOptix results.
Gross profit for the first quarter of fiscal 2004 totaled $7.8 million, an
increase of $0.4 million, or 5%, from $7.4 million in the first quarter of
fiscal 2003. Gross profit as a percentage of sales for the first quarters of
fiscal 2004 and 2003 were 32% and 36%, respectively. The decrease in gross
profit as a percentage of sales is primarily due to the higher revenue related
to the development services agreement which carries a lower margin and quality
and manufacturing problems in the factory that delayed shipments and increased
our manufacturing costs in the fiscal 2004 quarter.
Research, development, and engineering expenses ("R&D") for the first quarter of
fiscal 2004 totaled $3.3 million, an increase of $0.3 million, or 10%, from $3.0
million in the comparable prior year period. The increase was primarily due to
costs associated with our Zygo Applied Optics group in Southern California,
which commenced operations in the second half of fiscal 2003.
Backlog at September 26, 2003 totaled $37.1 million, a decrease of $0.1 million,
or 0.3%, from $37.2 million at June 30, 2003. Backlog at September 26, 2003
decreased $5.8 million, or 14%, from $42.9 million at September 27, 2002. Orders
for the first quarter of fiscal 2004 totaled $24.1 million. Orders by segment
for the first quarter of fiscal 2004 consisted of $16.6 million, or 69%, in the
semiconductor segment and $7.5 million, or 31%, in the industrial segment.
The Company maintained cash, cash equivalents, and marketable securities at
September 26, 2003 totaling $48.5 million, a decrease of $4.4 million from June
30, 2003. The decrease was primarily due to purchases of capital equipment, an
increase in accounts receivable, payments of year-end accrued employee benefits,
the net loss for the quarter, and a decrease in progress payments.
Management's View
The first quarter of our fiscal year is traditionally weak. This quarter was no
exception. In addition, we encountered quality and manufacturing problems in the
factory that are being addressed and which we expect will have diminishing
effects over the next few quarters.
It was encouraging, however, in our recent trip to Taiwan to note that the flat
panel market continues to invest heavily in new fabs and technology. These
investments leverage our stage position metrology, our optics manufacturing, and
our microscope interferometry. We anticipate, in the second quarter, that we
will sign contracts that will begin to offset the startup costs associated with
our Zygo Applied Optics design team, established in April of this year.
We continue to see a number of major opportunities in the optics and metrology
sector. Our view of the markets, going forward, is significantly more positive
than at this time last year.
2
<Page>
ZYGO's teleconference to discuss the results of the first quarter of fiscal 2004
will be held at 6 PM Eastern Standard Time on October 30, 2003 and can be
accessed by dialing 800-633-8410. This call is web cast live on ZYGO's web site
at www.zygo.com. The call may also be accessed for 30 days following the
teleconference.
Zygo Corporation (NASDAQ: ZIGO), headquartered in Middlefield, Connecticut, is a
worldwide developer and supplier of high precision optics, optical assemblies,
high performance metrology instruments, and automation for the semiconductor and
industrial markets. See ZYGO's web site at WWW.ZYGO.COM for additional
information.
All statements other than statements of historical fact included in this news
release regarding our financial position, business strategy, plans, anticipated
growth rates, and objectives of management of the Company for future operations
are forward-looking statements. Forward-looking statements are intended to
provide management's current expectations or plans for the future operating and
financial performance of the Company based upon information currently available
and assumptions currently believed to be valid. Forward-looking statements can
be identified by the use of words such as "anticipate," "believe," "estimate,"
"expect," "intend," "plans," "strategy," "project," and other words of similar
meaning in connection with a discussion of future operating or financial
performance. Actual results could differ materially from those contemplated by
the forward-looking statements as a result of certain factors. Among the
important factors that could cause actual events to differ materially from those
in the forward-looking statements are fluctuations in capital spending in the
semiconductor industry, fluctuations in net sales to our major customer,
manufacturing and supplier risks, dependence on new product development, rapid
technological and market change, international operations, dependence on
proprietary technology and key personnel, length of the sales cycle,
environmental regulations, and changes in expected costs of discontinued
operations. Further information on potential factors that could affect Zygo
Corporation's business is described in our reports on file with the Securities
and Exchange Commission, including its Form 10-K for the fiscal year ended June
30, 2003.
3
<Page>
Zygo Corporation and Subsidiaries
Condensed Consolidated Statements of Operations
(Unaudited)
(Thousands, except per share amounts) Three Months Ended
---------------------------------------------------
September 26, September 27,
2003 2002
---- ----
Net sales $24,247 $ 20,409
Cost of goods sold 16,470 13,043
------- --------
Gross profit 7,777 7,366
Selling, general, and administrative expenses 5,838 5,564
Research, development, and engineering expenses 3,309 2,998
------- --------
Operating loss (1,370) (1,196)
Other income, net 249 59
------- --------
Loss from continuing operations
before income taxes and minority interest (1,121) (1,137)
Income tax benefit 448 432
Minority interest, net of tax 10 (143)
------- --------
Loss from continuing operations (663) (848)
------- --------
Discontinued TeraOptix operations, net of tax (162) (1,682)
Charges on the disposal of TeraOptix, net of tax - (9,352)
------- --------
Loss from discontinued operations (162) (11,034)
------- --------
Net loss $ (825) $(11,882)
======= ========
Basic - Loss per share:
Continuing operations $ (0.04) $ (0.05)
======= ========
Discontinued operations $ (0.01) $ (0.63)
======= ========
Net Loss $ (0.05) $ (0.68)
======= ========
Diluted - Loss per share:
Continuing operations $ (0.04) $ (0.05)
======= ========
Discontinued operations $ (0.01) $ (0.63)
======= ========
Net Loss $ (0.05) $ (0.68)
======= ========
Weighted average number of shares:
Basic and diluted 17,678 17,510
======= ========
4
<Page>
Zygo Corporation and Subsidiaries
Condensed Consolidated Balance Sheets
(Unaudited)
(Thousands of dollars) September 26, 2003 June 30, 2003
------------------ -----------------
Assets
Current assets:
Cash and cash equivalents $ 28,267 $ 31,209
Marketable securities 14,958 14,929
Receivables 14,249 12,868
Inventories 18,686 18,444
Prepaid expenses 1,586 1,791
Deferred income taxes 5,499 5,179
Assets from discontinued unit held for sale 11,899 11,899
------------ -----------
Total current assets 95,144 96,319
Marketable securities 5,298 6,712
Property, plant, and equipment, net 27,165 26,648
Deferred income taxes 27,424 26,364
Intangible assets, net 5,149 5,025
------------ -----------
Total assets $ 160,180 $ 161,068
============ ===========
Liabilities and Stockholders' Equity
Current liabilities:
Current portion of long-term debt $ 11,164 $ 11,374
Accounts payable 5,965 5,254
Accrued expenses and progress payments 8,513 11,060
Income taxes payable 1,642 1,750
------------ -----------
Total current liabilities 27,284 29,438
Other long term liabilities 525 609
Minority interest 1,151 1,161
Stockholders' equity 131,220 129,860
------------ -----------
Total liabilities and stockholders' equity $ 160,180 $ 161,068
============ ===========
5