Under controversial circumstances Annen was deselected for the 2009 election, losing a primary election to Danial Ilkhanipour by 45 votes to 44. Ilkhanipour lost the seat at the 2009 election to the CDU candidate Rüdiger Kruse. In March 2010, Annen joined the German Marshall Fund as a Senior Fellow in Washington, D.C., for a six-month term. Between 2011 and 2013, he served as director of European policy analysis at the Berlin headquarters of the Friedrich Ebert Foundation, whose aim is to promote democracy, political education, and promote students of outstanding intellectual abilities and personality