He played parts of two seasons in Major League Baseball (MLB) with the Toronto Blue Jays.

Thigpen was called up to the Blue Jays on June 5, 2007, and made his major-league debut the next day at Rogers Centre in Toronto against the Tampa Bay Devil Rays.

[6] During the 2008 season, Thigpen saw less playing time due to fellow catcher Rod Barajas coming to Toronto.

[6] On February 4, 2009, Thigpen was designated for assignment to clear a roster spot for newly acquired pitcher Brian Burres.

[9] On March 27, 2009, Thigpen was traded to the Oakland Athletics in exchange for a player to be named later or cash considerations.