Originally drafted by the Chicago Cubs in the 17th round of the 1998 amateur draft, Hinske was traded to the Oakland Athletics and Toronto Blue Jays before seeing big league play.
On December 7, 2001, Blue Jay General Manager J. P. Ricciardi acquired from Hinske and reliever Justin Miller from the Athletics for Billy Koch, a move designed to bring youth and vitality to the team. Hinske was inserted in the every day line-up in 2002, playing third base, and was a key contributor for the team hitting predominantly in the number two spot in the line-up. While criticized early for his sometimes shoddy defense, Hinske made up for his lapses with his bat, hitting 24 home runs, knocking in 84 runs and scoring 99 runs. He won the American League MLB Rookie of the Year award.
Hinske slumped through the early part of the 2003 season before disclosing that he had a broken bone in his right hand. After returning from the disabled list, he was unable to match his numbers of the previous year, batting just .243 with 12 home runs and 63 RBIs.