Although Glaus was converted from shortstop to third base in the minors (and played 10 games at shortstop for the Angels), he started at shortstop for the Toronto Blue Jays against the Chicago White Sox on May 26, 2006 due to the demotion of shortstop Russ Adams. Glaus was not expected to do much fielding due to the fact the pitcher that day was known to induce many fly balls, instead of ground balls. This defensive alignment didn't affect his hitting, collecting 2 hits with a home run. Since then, Glaus made several starts at shortstop, usually when Toronto was facing National League opponents at their home ballpark, where there is no DH.
After hitting 38 home runs and 104 RBI in the 2006 season, Glaus earned a single 10th place vote for the 2006 American League MVP Award.
In 2006, Glaus had the lowest zone rating of any Major League third baseman (.741).