Johnson was drafted by the Toronto Blue Jays in the 17th round of the 1999 MLB Draft. In the minors, he was a Southern League All-Star in 2001 with the Tennessee Smokies, while hitting .314 with 13 home runs and 74 RBI. Johnson made his Major League debut on April 17, 2003 against the New York Yankees as a pinch runner. He recorded his first major league hit on April 20, 2003 against Boston Red Sox pitcher Casey Fossum and his first home run on May 17, 2003 against Jeremy Affeldt of the Kansas City Royals . He finished his rookie season, with a .294 batting average, 10 home runs, and 52 runs batted in. Johnson also won the American League Rookie of the Month Award for the month of September.