The major change for automatic qualification dictates that one team from among the champions of Conference USA, Mid-American Conference, Mountain West Conference, Sun Belt Conference or the Western Athletic Conference earn automatic qualification if such team is ranked in the top 12 of the final BCS standings or such team is ranked in the top 16 of the final BCS standings and its ranking in the final BCS standings is higher than that of a champion of a conference that has an annual automatic berth.

In previous years, automatic qualification was earned for any team finishing sixth or higher in the final BCS standings.

If the 2006 automatic qualification standards had been in place, the following additional teams would have been guaranteed automatic selection to the BCS during the first eight seasons of the BCS: 1998 Tulane, No. 10, Conference USA; 1999 Marshall No. 12 , Mid-American; 2003 Miami (Ohio), No. 11, Mid-American.