The Philadelphia Phillies drafted Kendrick in the seventh round (205th overall) of the 2003 Major League Baseball Draft, which caused him to reject a football scholarship offer to Washington State University. Kendrick began his career in the lower levels of the minor league system, and struggled mightily. A feature article in "Phillies" magazine noted, Early in Kendrick's career, many within the organization questioned his work ethic and maturity, which they thought may have contributed to his underachievement. In 2006, however, the Phillies "patience was ... rewarded"; pitching for the Lakewood BlueClaws for the third consecutive season, he earned Phillies Minor League Pitcher of the Month accolades for May, thus warranting a promotion to the Clearwater Threshers. In 20 starts with Clearwater, Kendrick posted a 3.53 ERA, among the best in the Florida State League. This performance as well as the fact that he spent significant time working out and focusing on mechanical improvement allayed the previous fears of poor work ethic. Ultimately, 2007 would be Kendrick's last in the low levels of the Phillies' minor leagues, as he began the season with the Double-A (AA) Reading Phillies, and finished it with the big league club.