SOUTH SAN FRANCISCO, Calif. –– Fluidigm Corporation (NASDAQ:FLDM) today announced its financial results for the third quarter ended September 30, 2012.

Product revenue for the third quarter of 2012 was $12.6 million, an increase of 24% from $10.2 million in the third quarter of 2011. Product margin was a record 72% in the third quarter of 2012, up from 67% in the third quarter of 2011 and 69% in the second quarter of 2012. Total revenue for the third quarter of 2012 was $12.8 million, an increase of 21% from $10.6 million in the third quarter of 2011. Net loss for the third quarter of 2012 was $4.2 million, compared to a net loss of $4.5 million in the third quarter of 2011. Non-GAAP net loss for the third quarter of 2012 was $2.6 million, compared with the $3.1 million non-GAAP net loss for the third quarter of 2011 (see accompanying table for reconciliation of GAAP and non-GAAP measures).

“Our leadership in the emerging single-cell genomics market continued to be a major growth driver in Q3 as this market continued to show strength in a tough macro-environment. We believe growth occurred because our customers are making breakthroughs in many areas of research, including cancer, stem cells, immunology, and infectious disease. In an era of budget sequestration worries, researchers are recognizing that embracing the single-cell field with our market-leading products can be a differentiator. We are energized by how quickly the field is adopting the C1™ Single-Cell Auto Prep System – the level of interest in the C1 system has surpassed our expectations. We began shipping C1 systems in Q3 and have substantially filled the 25 Early Access Program (EAP) slots,” said Gajus Worthington, Fluidigm President and Chief Executive Officer.

“Q3 was another strong consumables quarter too,” he continued, “with growth of 57% fueled by higher pull-through from production customers and an increased installed base of over 605 systems at the end of the third quarter. A continued shift to our higher margin products helped drive very strong product margin performance of 72%.”

Financial Highlights and Analysis

Fluidigm ended Q3 with approximately $90 million in cash, after a successful and over-subscribed financing in August.

Instrument revenues grew 5% year-on-year in the quarter and 10% year-to-date, driven by adoption of Fluidigm’s broadening menu of single-cell genomics tools.

Consumables revenue grew 57% year-on-year, driven by robust sales of both genotyping and gene expression integrated fluidic circuits (IFCs).

Product margins climbed 5% year-on-year and 3% sequentially to a record 72% due primarily to a shift in mix of both consumables and instruments to higher margin products.

Consumables pull-through was within its historical range of $40,000 – $50,000 per instrument/year for analytical systems, and $10,000 – $15,000 per instrument/year for preparatory systems.

Geographic revenue as a percent of total product revenue was as follows: United States – 62%; Europe – 21%; Asia-Pacific – 10%; Japan – 6%; and Other – 1%.

Non-GAAP net loss narrowed to $2.6 million due to a combination of revenue growth, strong product margins, and operating expense control.

Business Highlights Since Fluidigm’s Last Earnings Release

Fluidigm’s instrument installed base passed the 600 mark during the quarter.

We began shipments of the new C1 system to EAP customers and have successfully installed systems at major research institutions in the United States, Asia and Europe.

Fluidigm introduced four new IFCs – the consumables that provide the application menu for the BioMark™ HD system – last week, which will significantly expand our customers’ capabilities in several key markets. The new IFCs are:

qdPCR 37K™ IFC for specialized high-throughput digital PCR.

High-Precision 96.96 Genotyping™ IFC for genotyping applications that require the industry’s highest call rates.

192.24 Gene Expression™ IFC for high-throughput gene expression applications.

And a completely new configurable chip architecture, the FLEXsix™ Gene Expression IFC, for flexible, targeted gene expression applications.

About half of the BioMark HD systems sold during the quarter were targeted for single-cell research.

Analytical systems (BioMark, BioMark HD and EP1™) represented approximately 70% of the installed base and preparatory systems (Access Array™ and C1 instruments) represented approximately the remaining 30%.

Access Array instrument sales grew sharply sequentially, but from a smaller base.

Financial Outlook

The Company currently expects full year 2012 product revenue to grow 24% to 26% over full year 2011 product revenue of $40.6 million. This range incorporates appropriate conservatism regarding customer buying behavior outside of our single-cell business prior to the impending federal budget sequestration decision. Fluidigm expects annual product revenue in 2012 to pass the $50 million mark for the first time in its history. In addition, 2012 grant revenue is expected to be approximately $0.6 million.

Conference Call Information

Fluidigm will host a conference call today, November 7, 2012 at 5:30 p.m. Eastern Time. The call can be accessed by calling (877) 556-5248 (domestic toll-free) or (720) 545-0029 (international toll). Fluidigm will also provide a live stream of its third quarter of 2012 financial results conference call for investors at: https://investors.fluidigm.com/events.cfm. The link will not be active until 5:15 p.m. Eastern Time on November 7, 2012. A telephone replay of the teleconference will be available 90 minutes after the end of the call at (855) 859-2056 (domestic toll-free), or (404) 537-3406 (international toll), access code 53675220. The conference call will also be archived on the Fluidigm investor’s page at: https://investors.fluidigm.com.