The qualification process was divided in three stages. In the first stage, the 34 teams were divided in 10 groups of three teams each and two groups of two teams each. Groups with three teams had two rounds, with the best ranked team according to FIFA in each group entering the competition in the second round. In each group, teams were paired 2-by-2 and played home-and-away matches.
The 12 winners of the first stage advanced to the second stage, where they were divided into three groups of four teams each. Teams in each group would play against each other home-and-away, and the two teams with most points in each group would advance to the Final Round.
In the third stage, the six teams were put in a single group, and played against each other home-and-away. The three teams with most points qualified to the World Cup. The fourth placed team advanced to the AFC–CONCACAF play-off against the winner of a play-off between third placed teams in the Third Round of Asia.
The First and Second Rounds reduced the 34 entrants to 24 and 12 teams, respectively. The remaining 12 teams were then placed into three Third Round groups of four, with the top two teams in each group advancing to the Fourth and final qualification group. The Third Round began in August 2004 and ended in November 2004. The top three teams from the Fourth Round group of six (held from February 2005 to October 2005) qualified for the 2006 FIFA World Cup. The fourth-placed team competed in a home-and-away play-off against the fifth-placed team from Asia.