On December 29, 2008, Helicos BioSciences Corporation ("Helicos" or the "Company") executed the Third Amendment to the Loan and Security Agreement (the "Third Amendment") among Helicos, certain lenders (the "Lenders") and General Electric Capital Corporation ("GE"), dated as of December 29, 2008. The Third Amendment amends the Loan and Security Agreement (the "Loan Agreement") among Helicos, the Lenders and GE, dated as of December 31, 2007, as amended by the Second Amendment to the Loan and Security Agreement (the "Second Amendment"), dated as of June 27, 2008, which provided for a $20 million senior secured term credit facility (the "Credit Facility"). The Loan Agreement was previously filed with the Company's annual report on Form 10-K filed with the Securities and Exchange Commission (the "SEC") on March 17, 2008. The Second Amendment was previously filed on the Company's Current Report on Form 8-k filed with the SEC on June 30, 2008.

The Third Amendment amends the prepayment provisions of the Loan Agreement to allow Helicos to make a prepayment of $10,000,000 (the "Pay Down Amount") without incurring any prepayment penalties. Pursuant to the Third Amendment, Helicos will make a prepayment, equal to the Pay Down Amount, on or before December 31, 2008. In connection with such prepayment, and in lieu of the 4% final payment fee with respect to the Pay Down Amount, the Third Amendment provides that Helicos will pay a fee equal to 2% of the initial $10 million term loan, payable on the earlier of (a) January 31, 2011 and (b) the maturity date for the Subsequent Term Loan made to Helicos pursuant to the Second Amendment.

The Third Amendment further provides that the obligations of the Company under the Loan Agreement, as amended, are no longer secured by a cash amount of $10,000,000. Such obligations continue to be secured under various collateral documents by interests in substantially all of the Company's personal property, including the pledge of the stock of the Company's wholly-owned subsidiary, and proceeds of any intellectual property, but not by the Company's intellectual property.

The foregoing description of the Third Amendment is qualified in its entirety by reference to the Third Amendment, a copy of which is included as Exhibit 10.1 to this report and is hereby incorporated by reference.

Item 9.01      Financial Statements and Exhibits

       (d)     Exhibits

Exhibit No.                                 Description

   10.1        Third Amendment to the Loan and Security Agreement among Helicos, the
               Lenders and General Electric Capital Corporation, dated as of
               December 29, 2008

   10.2        Loan and Security Agreement by and between the Registrant and General
               Electric Capital Corporation, dated December 31, 2007.