In 2006 the Blue Jays signed Burnett to a 3 year $31 million contract with the player opt out option after the 3rd year. They were taking a chance because of Burnett’s medical history. This came to fruition in the beginning of 2006. The year started with Burnett going on the disabled list with a piece of scar tissue from his Tommy John surgery. He came back from the disabled list, pitched 4 innings and went on the disability list again for two months. He finished the year strong but won only 10 games. 2007 found Burnett on the disabled list two more times. He finished the year 10-8 for the second straight year.
For the Blue Jays, this contract yielded great results in one of the three years. The other two years he only won 10 games. The Blue Jays paid $33 million to Burnett for that time which included periodic disabilities. After a year in which he won 18 games, he left the team for more money to join a division rival Yankees.