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The first leg was played on either the 11th, 12th, 13th or 15 August 2008. The second leg was held on either the 25th or 26 August 2008. The winners advanced to the First Round.
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Somalia | walkover | Niger | 0 - 2 | W/O |
| Mauritania | 0 - 2 | Guinea Bissau | 0 - 1 | 0 - 1 |
| Sierra Leone | walkover | Liberia | W/O | W/O |
| Tanzania | walkover | Congo DR | W/O | W/O |
| Lesotho | 1 - 9 | Namibia | 0 - 5 | 1 - 4 |
| Réunion | 7 - 0 | Seychelles | 4 - 0 | 3 - 0 |
| Malawi | 5 - 0 | Mozambique | 4 - 0 | 1 - 0 |
| Rwanda | 4 - 3 | Kenya | 2 - 2 | 2 - 1 |
The First Round first leg matches were held on the 29th, 30 and 31 June and 6th and 14 September 2008. The second legs were held on the 12th, 13th, 14th and 26 September 2008. The winners qualified for the Second Round.
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Zimbabwe | 2 - 1 | Réunion | 2 - 0 | 0 - 1 |
| Ghana | 5 - 1 | Libya | 3 - 0 | 2 - 1 |
| Tunisia | 1 - 3 | Burkina Faso | 0 - 0 | 1 - 3 |
| South Africa | 1 - 3 | Malawi | 0 - 1 | 1 - 2 |
| Mali | 1 - 2 | Niger | 1 - 0 | 0 - 2 |
| Nigeria | 2 - 3 | Benin | 2 - 0 | 0 - 3 |
| Cameroon | 2 - 1 | Gabon | 2 - 0 | 0 - 1 |
| Gambia | 7 - 1 | Sierra Leone | 4 - 1 | 3 - 0 |
| Sudan | 1 - 6 | Rwanda | 1 - 2 | 0 - 4 |
| Côte d'Ivoire | walkover | Senegal | W/O | W/O |
| Guinea | 2 - 2 | Guinea Bissau | 2 - 1 | 0 - 1 |
| Eritrea | walkover | Congo DR | W/O | W/O |
| Zambia | 0 - 0 (2-4 PSO) | Namibia | 0 - 0 | 0 - 0 |
| Angola | 4 - 1 | Botswana | 2 - 0 | 2 - 1 |
The first legs were played on the 7th, 8th and 9 November. The second legs were played on the 21st, 22nd and 23 November. The winners qualified for the Finals.
| Team 1 | Agg. | Team 2 | 1st leg | 2nd leg |
|---|---|---|---|---|
| Burkina Faso | 3 - 2 | Rwanda | 2 - 1 | 1 - 1 |
| Angola | 2 - 4 | Zimbabwe | 2 - 3 | 0 - 1 |
| Namibia | 3 - 8 | Malawi | 2 - 1 | 1 - 7 |
| Côte d'Ivoire | 2 - 2 | Niger | 2 - 1 | 0 - 1 |
| Ghana | 3 - 3 | Gambia | 3 - 1 | 0 - 2 |
| Guinea | 1 - 1 (4-3 PSO) | Benin | 1 - 0 | 0 - 1 |
| Eritrea | 0 - 5 | Cameroon | 0 - 2 | 0 - 3 |
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