Exhibit 10.3

SECOND AMENDMENT TO

ZYMOGENETICS

DEFERRED COMPENSATION PLAN FOR KEY EMPLOYEES

This Amendment is made to the ZymoGenetics Deferred Compensation Plan for Key
Employees (the “Plan”) which was originally effective November 1, 1992 and most
recently amended and restated effective November 1, 1997.

Effective January 1, 2006, the first sentence of Article III.2(a) is amended by
increasing the maximum percentage of salary a Participant may defer from 15% to
50%.

IN WITNESS WHEREOF, ZymoGenetics, Inc. has caused this Amendment to be executed
on the date indicated below.

 

    ZYMOGENETICS, INC. Dated: May 2, 2008     By:   /s/ Bruce L.A. Carter      
  Bruce L.A. Carter       Its:   Chairman and Chief Executive Officer