44 Asian teams are affiliated with FIFA, but Cambodia, Philippines, Bhutan and Brunei decided not to take part, and Myanmar was banned from the competition (for refusing to play a qualifier in Iran during 2002 qualifying), so a total of 39 teams took part, competing for 4.5 places in the World Cup.
The qualification was composed of three rounds. Only the 14 last ranked teams according to FIFA took part in the Preliminary Round, where they were paired 2-by-2 and played home-and-away knock-out matches. The 7 winners joined the other 25 teams in the Second Round, where those 32 teams were divided in 8 groups of four teams each. The teams in each group would play against each other home-and-away, and the team with most points in each group would advance to the Third Round.
In the Third Round, the 8 remaining teams were divided in two groups of 4 teams each, that would again play against each other in a home-and-away basis. The two teams with most points in each group would qualify to the World Cup. The two third placed teams would play-off against each other home-and-away. Winner of this play-off would play against the fourth placed team in the Final Round of CONCACAF in an intercontinental play-off for a place in the World Cup.
In the second round, the 25 teams who received byes, as well as the 7 play-off round winners, were split into eight groups of four teams each. Teams played home-and-away games with the other teams in their group, and the top-ranked team qualified for the third round.
In the third round, the 8 teams who won their groups in the earlier round were split into two groups of four teams each. Teams played home-and-away games with the other teams in their group, and the top two teams qualified for the 2006 FIFA World Cup. Meanwhile, the third-placed teams entered a play-off to determine who would contest the AFC–CONCACAF play-off.
Teams finishing 3rd in the third round groups played each other to determine a possible 5th qualifier from Asia. The first leg was originally played on 3 September 2005 but the match was ordered to be replayed by FIFA after a refereeing mistake. With Uzbekistan leading the tie 1-0, a penalty was awarded to them but the referee disallowed the resulting goal and offered an indirect freekick to Bahrain for encroachment. Uzbekistan had formally requested for the match to be recorded as an automatic 3-0 victory.
The Fourth Round winner then played the fourth-placed team of the CONCACAF qualifying group, Trinidad and Tobago, in a home-and-away play-off. The winner of this play-off qualified for the 2006 FIFA World Cup finals.