In the Second Round, the 30 teams were divided in 5 groups of 6 teams each. Teams in each group would play against each other in a home-and-away basis. The team with most points in each group would qualify to the World Cup.
The competition also constituted the qualification competition for the 2006 African Nations Cup with the top three nations of each group qualifying (except for Egypt, which qualifies as the host nation, the fourth nation in Egypt's group qualifying in Egypt's place).
The African qualifying zone saw 4 out of 5 finals places going to World Cup debutants (Angola, Togo, Côte d'Ivoire and Ghana). Nigeria missed out on a fourth consecutive finals appearance while Cameroon did not reach their fifth consecutive finals.
The African zone also featured a group of death — Group 3, which brought together Africa's most frequent World Cup qualifier Cameroon with the two eventual finalists of the 2006 Africa Cup of Nations: Egypt and the Ivory Coast.