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In 2009, Kratz signed with the Pirates, who were in need of a primary Triple-A catcher after the call-up of Robinzon Diaz to replace the injured Ryan Doumit. Kratz played the 2009 season with the Indianapolis Indians and finished batting .273/.337/.470, with 11 home runs, and 43 RBI. He was named an IL Mid-Season All-Star, the IL Triple-A All-Star Game Top Star (on July 15), and an IL Post-Season All-Star (on September 1).