| 1 | Kenenisa Bekele | ETH | 13:38,03 | Q | |
| 2 | Eliud Kipchoge | KEN | 13:38,73 | Q | |
| 3 | John Kibowen | KEN | 13:40,72 | Q | |
| 4 | Abderrahim Goumri | MAR | 13:42,09 | Q | |
| 5 | Juan Carlos de la Ossa | ESP | 13:42,23 | Q | |
| 6 | Zersenay Tadesse | ERI | 13:42,41 | q | |
| 7 | Boniface Kiprop | UGA | 13:42,88 | ||
| 8 | Salah Hissou | MAR | 13:44,27 | ||
| 9 | Erik Sjöqvist | SWE | 13:55,89 | ||
| 10 | Khoudir Aggoune | ALG | 13:56,41 | ||
| 11 | Yawo Kloutse | TOG | 14:45,85 | NR | |
| Cathal Lombard | IRL | DNS | |||
| Michael Aish | NZL | DNS | |||
| Fabian Joseph | TAN | DNS |
| 1 | Gebre-egziabher Gebremariam | ETH | 13:32,46 | Q |
| 2 | Abraham Chebii | KEN | 13:32,54 | Q |
| 3 | Richard Limo | KEN | 13:32,82 | Q |
| 4 | Hicham El Guerrouj | MAR | 13:32,88 | Q |
| 5 | Abiyote Abate | ETH | 13:33,24 | Q |
| 6 | Moukheld Al-Outaibi | KSA | 13:33,91 | q |
| 7 | Christian Belz | SUI | 13:36,54 | q |
| 8 | Alejandro Suárez | MEX | 13:41,97 | q |
| 9 | Jorge Torres | USA | 13:42,42 | q |
| 10 | Abdelhak Zakaria | BRN | 13:44,15 | |
| 11 | Hassan Mourhit | BEL | 14:09,14 | |
| 12 | Eduardo Buenavista | PHI | 14:12,55 | |
| Kamiel Maase | NED | DNS | ||
| John Yuda | TAN | DNS | ||
| Abdullah Ahmad Hassan | QAT | DNS |