Exhibit 10.12

SECOND AMENDMENT

TO

LOAN AND SECURITY AGREEMENT

THIS SECOND AMENDMENTto Loan and Security Agreement (this Amendment) is entered into this 23rdday of March, 2009, by
and between Silicon Valley Bank (Bank) and ARCA biopharma Colorado, Inc.(f/k/a ARCA biopharma, Inc.), a Delaware corporation (Borrower) whose address is 8001 Arista Place, Suite 200, Broomfield, CO 80021.

RECITALS

A.Bank and Borrower have entered into that certain Loan and Security Agreement dated as of July 17, 2007, as amended by a First Amendment, dated January 23, 2009 (as the same may from time to time be further amended, modified,
supplemented or restated, the Loan Agreement).

B.Bank has extended credit to Borrower for the purposes permitted in
the Loan Agreement.

C.Borrower has requested that Bank amend the Loan Agreement to revise the maturity date of the outstanding GC
Line B Advances.

D.Bank has agreed to so amend certain provisions of the Loan Agreement, but only to the extent, in accordance
with the terms, subject to the conditions and in reliance upon the representations and warranties set forth below.

AGREEMENT

NOW, THEREFORE, in consideration of the foregoing recitals
and other good and valuable consideration, the receipt and adequacy of which is hereby acknowledged, and intending to be legally bound, the parties hereto agree as follows:

1. Definitions. Capitalized terms used but not defined in this Amendment shall have the meanings given to them in the Loan Agreement.

2. Amendment to Loan Agreement. The definition of GC Line B Tranche Two maturity Date in Section 13.1 of the Loan Agreement is
hereby deleted in its entirety and replaced with the following:

GC Line B Tranche Two Maturity Date is
April 6, 2009.

3. Limitation of Amendment.

3.1The amendment set forth in Section 2, above, is effective for the purposes set forth herein and shall be limited precisely as written and shall not be deemed to (a) be a consent to any amendment,
waiver or modification of any other term or condition of any Loan Document, or (b) otherwise prejudice any right or remedy which Bank may now have or may have in the future under or in connection with any Loan Document.

3.2This Amendment shall be construed in connection with and as part of the Loan Documents and all terms, conditions, representations, warranties,
covenants and agreements set forth in the Loan Documents, except as herein amended, are hereby ratified and confirmed and shall remain in full force and effect.



---

4. Representations and Warranties. To induce Bank to enter into this Amendment, Borrower hereby
represents and warrants to Bank as follows:

4.1Immediately after giving effect to this Amendment (a) the representations and
warranties contained in the Loan Documents are true, accurate and complete in all material respects as of the date hereof (except to the extent such representations and warranties relate to an earlier date, in which case they are true and correct as
of such date), and (b) no Event of Default has occurred and is continuing;

4.2Borrower has the power and authority to execute
and deliver this Amendment and to perform its obligations under the Loan Agreement, as amended by this Amendment;

4.3The
organizational documents of Borrower previously delivered to Bank remain true, accurate and complete and have not been amended, supplemented or restated and are and continue to be in full force and effect;

4.4The execution and delivery by Borrower of this Amendment and the performance by Borrower of its obligations under the Loan Agreement, as
amended by this Amendment, have been duly authorized;

4.5The execution and delivery by Borrower of this Amendment and the
performance by Borrower of its obligations under the Loan Agreement, as amended by this Amendment, do not and will not contravene (a) any law or regulation binding on or affecting Borrower, (b) any contractual restriction with a Person
binding on Borrower, (c) any order, judgment or decree of any court or other governmental or public body or authority, or subdivision thereof, binding on Borrower, or (d) the organizational documents of Borrower;

4.6The execution and delivery by Borrower of this Amendment and the performance by Borrower of its obligations under the Loan Agreement, as
amended by this Amendment, do not require any order, consent, approval, license, authorization or validation of, or filing, recording or registration with, or exemption by any governmental or public body or authority, or subdivision thereof, binding
on either Borrower, except as already has been obtained or made; and

4.7This Amendment has been duly executed and delivered by
Borrower and is the binding obligation of Borrower, enforceable against Borrower in accordance with its terms, except as such enforceability may be limited by bankruptcy, insolvency, reorganization, liquidation, moratorium or other similar laws of
general application and equitable principles relating to or affecting creditors rights.

5. Counterparts. This Amendment may
be executed in any number of counterparts and all of such counterparts taken together shall be deemed to constitute one and the same instrument.

6. Effectiveness. This Amendment shall be deemed effective upon (a) the due execution and delivery to Bank of this Amendment by each party hereto and (b) Borrowers payment of all Bank Expenses in connection herewith.

[Signature page follows.]



2



---

IN WITNESS WHEREOF,the parties hereto have caused
this Amendment to be duly executed and delivered as of the date first written above.



|                    |  |                    |  |                               |  |     |  |                    
|------------------- |  | ------------------ |  | ----------------------------- |  | --- |  | -------------------
|BANK:               |  |                    |  | BORROWER:                    
|                    |  |                   
|SILICON VALLEY BANK |  |                    |  | ARCA BIOPHARMA COLORADO, INC.
|                    |  |                    |  |                              
|By:                 |  | /s/ Bret J. Turner |  |                               |  | By: |  | /s/ Patrick Wheeler

|            |  |                |  |  |  |             |  |                
|----------- |  | -------------- |  |  |  | ----------- |  | ---------------
|Print Name: |  | Bret J. Turner |  |  |  | Print Name: |  | Patrick Wheeler

|       |  |                      |  |  |  |        |  |            
|------ |  | -------------------- |  |  |  | ------ |  | -----------
|Title: |  | Relationship Manager |  |  |  | Title: |  | SVP Finance



3