Kafes made his debut in the national team against Croatia in April 2001 and scored his first goal against Austria in Vienna in March 2003. Kafes made two appearances in UEFA EURO 2004 qualifying, and was in the finals squad and he won Euro 2004 with Greece. Kafes participated in 2006 World Cup qualifying campaign, the 2005 FIFA Confederations Cup. Kafes has been re-called into the team from the new coach Fernando Santos during the qualification for Euro 2012. On 8 October 2010 Kafes came on as a substitute against Latvia replacing Giorgos Karagounis, helping the team to qualify for UEFA's 2012 European Football Championship tournament. This was Kafes' first competitive match under new coach Fernando Santos. On 17 November 2010, Kafes played also the second half of the friendly match against Austria, giving a big contribution, where Greece beat Austria.