The 2006 Toronto Blue Jays season was the franchise's thirtieth season of Major League Baseball. It resulted in the Blue Jays finishing second in the American League East with a record of 87 wins and 75 losses. For the second straight season, Blue Jays hitters combined for fewer than 1,000 strikeouts. It was the first time since the team's World Series championships in 1992 and 1993 that the Blue Jays had combined for fewer than 1,000 strikeouts in consecutive 162-game seasons, as well as the only season since 1993 (as of 2012) that the team finished above third place in its division.
On January 3, J.P. Ricciardi signed free-agent catcher Jason Phillips to a minor league contract. 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. Quiroz was later claimed on waivers by the Seattle Mariners, and Phillips started the season with the team after Gregg Zaun was put on the disabled list.
The trades for Troy Glaus and Lyle Overbay in the off-season created a glut of corner infielders for the Jays, as the team now had five players (Glaus, Overbay, Eric Hinske, Corey Koskie, and Shea Hillenbrand) who could play third base, first base, or designated hitter. The Jays relieved some of this pressure on January 6, by trading Koskie to the Milwaukee Brewers in the second deal between the two clubs in less than a month. The Blue Jays received minor league pitcher Brian Wolfe in return for Koskie. The Blue Jays also moved first baseman (and former third baseman) Eric Hinske to right field as a result.
On February 6, Toronto signed former Angels catcher Bengie Molina to a one-year contract with an option for a second. Three days later, Toronto wrapped up its off season moves by re-signing Shea Hillenbrand and Pete Walker, each to a one-year deal.
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. However, Rios would not compete in the game due to a serious staph infection that occurred around June 28, possibly as the result of a foul ball off Rios' leg during a game on June 27. Manager John Gibbons was also picked as an assistant coach for the AL team. The five Blue Jay players selected to the AL All-Star team was the most to appear in an All-Star Game since 1993. The only AL team with more All-Stars than the Jays was the World Series champion the Chicago White Sox, with six.
On July 7, Troy Glaus was picked to compete in the 2006 Home Run Derby, though during the Derby, he hit only one home run and was eliminated after the first round.
On July 19, infielder Shea Hillenbrand was designated for assignment after an altercation with the team management. Shortly after Hillenbrand, along with reliever Vinnie Chulk, was traded to the San Francisco Giants for reliever Jeremy Accardo.
On August 3, rookie second baseman Ryan Roberts started his first game in the MLB, and had his first hit, which was a home run. He is one of few Blue Jays rookies to have his first hit a home run in his first start.
On August 12, the Blue Jays got the Minnesota Twins to hit into 6 double plays, tying a Blue Jays record set on April 16, 1996. (Blue Jays vs. Detroit).
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. An argument ensued on the mound, in front of the audience at the Rogers Centre. Lilly eventually did leave the game and then headed into the clubhouse. Gibbons subsequently followed him into the hallway, where it appeared to eyewitnesses that he and Lilly got into a fight. Numerous team members and support personnel rushed into the tunnel to break them up. After the game, both the pitcher and manager denied any altercation and said the problem had been resolved.
Despite their on-field and off-field problems, the Blue Jays managed to play well in the critical month of September, going 18–10. 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. This marked the first time that the Jays had finished above third place in their division since their World Championship season of 1993, and with the most wins since the 1998 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 November 28, the Blue Jays announced that they had re-signed catcher Gregg Zaun to a two-year contract with an option for 2009.
On December 18, the Blue Jays announced that they had re-signed centre fielderVernon Wells to a seven-year contract worth $126 million, to come into effect after the 2007 season. It was the largest contract in club history.