| 1 | Kenenisa Bekele | ETH | 13:19,77 | Q | |
| 2 | Matthew Tegenkamp | USA | 13:19,87 | Q | |
| 3 | Mohammed Farah | GBR | 13:19,94 | Q | |
| 4 | Vincent Kiprop Chepkok | KEN | 13:20,24 | Q | |
| 5 | Jesús España | ESP | 13:20,40 | Q | |
| 6 | Chris Solinsky | USA | 13:20,64 | q | |
| 7 | Joseph Ebuya | KEN | 13:22,41 | q | |
| 8 | Anis Selmouni | MAR | 13:22,95 | q | |
| 9 | Teklemariam Medhin | ERI | 13:23,48 | q | |
| 10 | Collis Birmingham | AUS | 13:23,48 | q | |
| 11 | Saif Saaeed Shaheen | QAT | 13:26,35 | ||
| 12 | Geofrey Kusuro | UGA | 13:28,48 | ||
| 13 | Ali Abdosh | ETH | 13:36,52 | q (*) | |
| 14 | Daniele Meucci | ITA | 13:37,79 | ||
| 15 | Etienne Bizimana | BDI | 14:06,02 | ||
| 16 | Yuichiro Ueno | JPN | 14:30,76 | ||
| Bayron Piedra | ECU | DNF | |||
| Juan Luis Barrios | MEX | DNS | |||
| Fabiano Joseph Naasi | TAN | DNS |
* ... nach Protest für das Finale qualifiziert
| 1 | Moses Ndiema Kipsiro | UGA | 13:22,98 | Q | |
| 2 | Eliud Kipchoge | KEN | 13:23,34 | Q | |
| 3 | James Kwalia C'Kurui | QAT | 13:23,57 | Q | |
| 4 | Bernard Lagat | USA | 13:23,73 | Q | |
| 5 | Chakir Boujattaoui | MAR | 13:23,83 | Q | |
| 6 | Bekana Daba | ETH | 13:23,86 | ||
| 7 | Samuel Tsegay | ERI | 13:26,78 | ||
| 8 | Morhad Amdouni | FRA | 13:29,64 | ||
| 9 | Kidane Tadasse | ERI | 13:30,85 | ||
| 10 | Alemayehu Bezabeh | ESP | 13:33,52 | ||
| 11 | Evan Jager | USA | 13:39,80 | ||
| 12 | Hussain Jamaan Alhamdah | KSA | 13:44,59 | ||
| 13 | Alistair Ian Cragg | IRL | 13:46,34 | ||
| 14 | Arne Gabius | GER | 13:49,13 | ||
| 15 | Moses Kibet | UGA | 13:52,38 | ||
| 16 | Sergio Sánchez | ESP | 13:53,51 | ||
| 17 | Marco Joseph | TAN | 13:53,67 | ||
| 18 | Tonny Wamulwa | ZAM | 14:01,67 | ||
| 19 | Mohamed Ali Mohamed | SOM | 14:34,62 | ||
| 20 | Omar Abusaid | PLE | 15:14,88 |