 Clippard was drafted in the ninth round of the 2003 MLB draft, with the 274th overall selection, by the New York Yankees.Though he had signed a National Letter of Intent in the fall of 2002 to attend the University of South Florida on a baseball scholarship, allowing him to play college baseball for the South Florida Bulls, he chose to turn professional due to his draft position and the opportunity to play for the Yankees.Clippard made his professional debut that year in the Rookie-level Gulf Coast League (GCL) with the GCL Yankees, pitching to a 3–3 win–loss record with a 2.89 ERA.