| Friday 7th April 2000 | |||
| 1st Leg | |||
| Djibouti | 1-1 | Congo DR | |
| Mauritania | 1-2 | Tunisia | |
| Saturday 8th April 2000 | |||
| 1st Leg | |||
| Botswana | 0-1 | Zambia | |
| Guinea-Bissau | 0-0 | Togo | |
| Madagascar | 2-0 | Gabon | |
| Malawi | 2-0 | Kenya | |
| Seychelles | 1-1 | Namibia | |
| Tanzania | 0-1 | Ghana | |
| Uganda | 4-4 | Guinea | |
| Sunday 9th April 2000 | |||
| 1st Leg | |||
| Benin | 1-1 | Senegal | |
| Cape Verde Islands | 0-0 | Algeria | |
| Central African Rep | 0-1 | Zimbabwe | |
| Chad | 0-1 | Liberia | |
| Equatorial Guinea | 1-3 | Congo | |
| Eritrea | 0-0 | Nigeria | |
| Ethiopia | 2-1 | Burkina Faso | |
| Gambia | 0-1 | Morocco | |
| Lesotho | 0-2 | South Africa | |
| Libya | 3-0 | Mali | |
| Rwanda | 2-2 | Ivory Coast | |
| Sao Tome e Principe | 2-0 | Sierra Leone | |
| Sudan | 1-0 | Mozambique | |
| Swaziland | 0-1 | Angola | |
| Wednesday 19th April 2000 | |||
| 1st Leg | |||
| Cameroon | 3-0 | Somalia | |
| Thursday 20th April 2000 | |||
| 1st Leg | |||
| Egypt | 2-0 | Mauritius | |
| Friday 21st April 2000 | |||
| 2nd Leg | |||
| Algeria | 2-0 | Cape Verde Islands | (2-0) |
| Saturday 22nd April 2000 | |||
| 2nd Leg | |||
| Gabon | 1-0 | Madagascar | (1-2) |
| Kenya | 0-0 | Malawi | (0-2) |
| Morocco | 2-0 | Gambia | (3-0) |
| Namibia | 3-0 | Seychelles | (4-1) |
| Nigeria | 4-0 | Eritrea | (4-0) |
| Sierra Leone | 4-0 | Sao Tome e Principe | (4-2) |
| South Africa | 1-0 | Lesotho | (3-0) |
| Tunisia | 3-0 | Mauritania | (5-1) |
| Zambia | 1-0 | Botswana | (2-0) |
| Sunday 23rd April 2000 | |||
| 2nd Leg | |||
| Angola | 7-1 | Swaziland | (8-1) |
| Burkina Faso | 3-0 | Ethiopia | (4-2) |
| Cameroon | 3-0 | Somalia | (6-0) |
| Congo | 2-1 | Equatorial Guinea | (5-2) |
| Congo DR | 9-1 | Djibouti | (10-2) |
| Egypt | 4-2 | Mauritius | (6-2) |
| Ghana | 3-2 | Tanzania | (4-2) |
| Guinea | 3-0 | Uganda | (7-4) |
| Ivory Coast | 2-0 | Rwanda | (4-2) |
| Liberia | 0-0 | Chad | (1-0) |
| Mali | 3-1 | Libya | (3-4) |
| Mozambique | 2-1 | Sudan | (2-2) |
| (Sudan won on away goals) | |||
| Senegal | 1-0 | Benin | (2-1) |
| Togo | 3-0 | Guinea-Bissau | (3-0) |
| Zimbabwe | 3-1 | Central African Rep | (4-1) |
