In total, 53 nations participated; however, due to the presence of the two tournaments' respective hosts, 52 teams were involved in each competition. South Africa qualified automatically as host for the World Cup, and Angola qualified as host for the African Cup of Nations. Both nevertheless competed in the qualifying phase to attempt to qualify for the other tournament.
Five knockout ties were originally required, involving the ten lowest ranked African countries (based on FIFA rankings as of July 2007). The actual draw was apparently conducted one day before the format was announced by CAF. The pairings were:
São Tomé and Príncipe and the Central African Republic both withdrew in early September. As a result, Swaziland and Seychelles (the highest ranked of the ten nations) were no longer required to play in this round, and the teams they were originally matched against, Somalia and Djibouti, were redrawn to play each other instead. The tie between Djibouti and Somalia was played as a one leg tie in Djibouti, as Somalia was not deemed suitable for FIFA matches; the other two ties were played as two leg ties.
The 48 qualifiers (45 direct entrants plus 3 winners of the first round) were split into 12 groups of 4 in the draw held in Durban, South Africa on 25 November 2007. Teams in each group played a home-and-away round-robin in 2008, with the 12 groups winners and 8 best runners-up advancing to the third round. As not all groups were of equal size after the exclusion of Ethiopia and the withdrawal of Eritrea, when ranking the runners-up, their results against their group's 4th placed team would not be counted.
Angola and Uganda are ranked by their overall goal difference.
Note: Angola were automatically qualified as hosts of the 2010 African Cup of Nations. However, they were subject to the same rules as other nations for continuation to the next stage of the qualifiers. Failure to advance from this group eliminated them from the qualifiers for the 2010 FIFA World Cup.
South Africa and Sierra Leone are ranked by their overall goal difference.
Note: South Africa were automatically qualified as hosts of the 2010 FIFA World Cup. However, they were subject to the same rules as other nations for continuation to the next stage of the qualifiers. Failure to advance from this group eliminated them from the qualifiers for the 2010 African Cup of Nations.
Morocco and Rwanda are ranked by their overall goal difference.
Ethiopia played four matches in this group, before FIFA announced the immediate suspension of the Ethiopian Football Federation (EFF) on 29 July 2008. On 12 September 2008, FIFA excluded the EFF from the 2010 World Cup qualifiers and the results of their matches were cancelled. While it was not clear if they were also explicitly excluded from the 2010 African Cup of Nations, their failure to complete the remaining fixtures effectively eliminated them from the tournament.
Chad was disqualified from the 2010 African Nations Cup qualifiers after failing to show up for their away match against Sudan, despite security guarantees. The match was subsequently rescheduled. Only matches between Mali, Sudan and Congo were taken into account for the qualification of the second round of the preliminaries of the African Cup of Nations. However, Chad was still able qualify for the 2010 FIFA World Cup. This could have led to complications if Chad had advanced to the next round or if Chad's exclusion the now alternate group standings had produced different group winners and impacted on the ranking of the second-placed side.
Along with the 12 group winners, the 8 highest-ranked runners-up also advanced to the third round. Because not all groups contained an equal number of teams, only results against the first- and third-placed teams in each group counted.
The 20 remaining sides were split into five groups of four. The draw for the groups took place on 22 October 2008 in Zürich, Switzerland.
The five group winners will qualify for the FIFA World Cup and the African Cup of Nations in 2010. Together with them, the five runners-up and the five third-placed teams qualify for the African Cup of Nations.