A native of Mesa, Arizona, Hillenbrand attended Mount View High School there, excelling in both baseball, as a shortstop, and soccer. He attended Mesa Community College from 1994-96, before being drafted by Boston in the 10th round of the 1996 amateur draft.

Hillenbrand played 72 games in 1996 for the Low-A Lowell Spinners in the New York - Penn League. In 1997, he was promoted to the Sarasota Red Sox of the Florida State League, and was promoted again after 57 games, finishing the season with 64 games with the Michigan Battle Cats of the Midwest League. Despite being drafted as a shortstop, he played at first base and third base his first two years in the minors.

In 1998, still with Michigan, he was converted to play catcher and responded with his best season in the minors, with a .349 batting average and 19 home runs. This earned him a promotion in 1999 to AA Trenton Thunder of the Eastern League. However, a leg injury restricted him to only 69 games.

The year 2000 saw Hillenbrand back at Trenton, now back to playing first base and third base as the injury prevented him from catching. An average season at age 25 did not bode well for his chances as a prospect, but he parlayed an invitation to spring training with the Red Sox in 2001 into a spot on the big-league team for opening day. Hillenbrand played 139 games for the Sox in his rookie season, mostly at third base, but a .263 batting average failed to hide his failure to get on base adequately (he had one of the lowest walks to plate appearances rates in the MLB), nor to hit with power. However, he retained his spot on the roster for 2002, and responded with a much better season, hitting 20 home runs with a .330 on base percentage and a .459 slugging average. His play earned him the starting third baseman spot in the All-Star Game.

Nevertheless, Hillenbrand entered 2003 being the subject of trade rumors. The Red Sox had signed free agent Bill Mueller, another third baseman, and many believed that Hillenbrand's lack of strike zone judgment would not be compatible with the on base percentage priorities of new Sox general manager Theo Epstein. With Mueller hitting around .380 and playing a solid third base, Hillenbrand became expendable and was sent to Arizona for pitcher Byung-Hyun Kim on May 29. He finished the season with a combined .280 batting average and career-highs in RBI (97) and home runs (20), including a three-homer game with the Diamondbacks in month of July.

In 2004, Hillenbrand hit a career-high .310 with 15 home runs and 80 RBI over 148 games. He was traded to the Blue Jays at the end of the season.

In a four-season career, Hillenbrand is a .288 hitter with 65 home runs and 309 in 577 games.