Phillips, who hit .238 the previous season for the Los Angeles Dodgers, also had an invitation to spring training, was supposed to have competed with Guillermo Quiróz for the role of the Blue Jays' backup catcher.
On July 2, Troy Glaus, Vernon Wells, Roy Halladay, B. J. Ryan, and Alex Ríos were picked to represent the Blue Jays at the Major League Baseball All-Star Game.
On August 16, the Blue Jays traded reliever Scott Schoeneweis to the Cincinnati Reds for cash considerations or a player to be named later (later announced to be INF Trevor Lawhorn).
On August 17, the Blue Jays traded first and third baseman and outfielder Eric Hinske and cash considerations to the Boston Red Sox for a player to be named later.
During a game against the Oakland Athletics on August 21, 2006, while on the verge of blowing an 8-run lead, John Gibbons walked to the mound to remove starter Ted Lilly.
This, combined with the slumping of the Boston Red Sox, enabled Toronto to snare sole possession of second place in the American League East by the end of the season.
On November 17, the Blue Jays announced that they had signed designated hitter Frank Thomas to a two-year contract worth $18 million, with an option for 2009.
On December 18, the Blue Jays announced that they had re-signed centre fielder Vernon Wells to a seven-year contract worth $126 million, to come into effect after the 2007 season.