The 2004 season ended with five undefeated teams vying for a spot in the national title game. In the 2003 season, no team finished the regular season unbeaten, and five teams finished the season with one loss. In 2004, the situation became even more complicated, as five teams went without losing, a record in the BCS era (later tied in 2009). USC of the Pac-10, Oklahoma of the Big 12, Auburn of the SEC, Utah of the MWC, and Boise State of the WAC all finished the regular season undefeated. USC and Oklahoma were ranked #1 and #2, respectively, in the preseason by both the AP and Coaches Polls, but the other three undefeated teams were handicapped by starting the season out of the top 15. Thus USC and OU played for the BCS National Championship in the Orange Bowl, while Auburn, Utah, and Boise State had to settle for other bowl games.

Auburn played in the Sugar Bowl and beat Virginia Tech, the ACC champion and ranked #8 by the BCS. Utah became the first BCS Buster and beat Pittsburgh, the champion of the Big East and ranked #21, in the Fiesta Bowl. Boise State lost a close, high scoring game in the Liberty Bowl to Louisville, the #10 ranked Conference USA champion.

As with previous seasons, fans of successful teams left out of BCS bowls were disappointed. Auburn, Utah, and Boise State all went unbeaten but were not offered a chance to compete for the BCS championship. Auburn was especially the focus of national media attention on this topic, since Auburn managed to go undefeated in the traditionally tough SEC. Adding to the frustration with the BCS system was the fact that Auburn and Utah, though both picked to play in BCS bowl games, would not be able to play each other as a match-up of highly ranked unbeatens. This confluence of events made 2004 a seminal year for serious momentum building behind a multi-team playoff system in college football, which would later be realized with the advent of the College Football Playoff.

USC was forced to vacate their BCS title win, along with their regular-season victory over rival UCLA, due to NCAA sanctions that stemmed from the USC athletics scandal. The AP title was not vacated, as the AP does not punish teams for violations. The severity of these sanctions has since been criticized by some pundits across college football.