The 2006 CIS football season began on September 2, 2006, and concluded with the 42nd Vanier Cup national championship on November 25 at Griffiths Stadium in Saskatoon, Saskatchewan, with the Laval Rouge et Or winning their fourth championship. Twenty-seven universities across Canada competed in CIS football this season, the highest level of amateur play in Canadian football, under the auspices of Canadian Interuniversity Sport (CIS).

Note: GP = Games Played, W = Wins, L = Losses, OTL = Overtime Losses, PF = Points For, PA = Points Against, Pts = Points

Teams in bold have earned playoff berths.

Ranks in italics are teams not ranked in the top 10 poll but received votes. NR = Not Ranked, received no votes.

The Vanier Cup is played between the champions of the Mitchell Bowl and the Uteck Bowl, the national semi-final games. In 2007, according to the rotating schedule, the winners of the Canada West conference Hardy Trophy meet the Ontario conference's Yates Cup champion for the Mitchell Bowl. The winners of the Atlantic conference Loney Bowl championship travel to the Dunsmore Cup Quebec championship team for the Uteck Bowl.

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