Hannahan attended Cretin-Derham Hall High School in Saint Paul, Minnesota, and also played football as a defensive back and earned All-Conference honors in basketball. He attended the University of Minnesota, where he played college baseball for the Minnesota Golden Gophers. He was named All-American. As a freshman, he hit .360 with 28 runs, nine doubles, four home runs and 30 RBIs in 1999.

In 2000 he batted .327 with 46 runs, 18 doubles, four triples, eight home runs, 43 RBIs and nine stolen bases during his sophomore season. He was named Big Ten Player of the Year and First-Team All-Big Ten during his junior season after hitting .372 with 65 runs, 20 doubles, four triples, 15 home runs, 63 RBIs and 16 stolen bases. He led the Big Ten Conference in runs, home runs and RBIs. Hannahan played for the Mankato Mashers of the Northwoods League, a collegiate summer league.

The Detroit Tigers selected Hannahan in the third round of the 2001 Major League Baseball draft. Hannahan made his major league debut on May 26, 2006, playing first base. He went 0-for-9 with the Tigers in 2006.

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