| Final A | Team | time | Rk. | | 1. Aleksandr Popov | RUS | 48.74s | 1. | | 2. Gary Hall, Jr. | USA | 48.81s | 2. | | 3. Gustavo Borges | BRA | 49.02s | 3. | | 4. Pieter van den Hoogenband | NED | 49.13s | 7. | | 5. Fernando Scherer | BRA | 49.57s | 4. | | 6. Pavlo Khnykin | UKR | 49.65s | 6. | | 7. Ricardo Busquets | PRO | 49.68s | 5. | | 8. Francisco Sánchez | VEN | 49.84s | 8. |
| Final B | Team | time | Rk. | | 9. Jon Olsen | USA | 49.80s | 12. | | 10.Christian-Alexander Tröger | GER | 49.90s | 10. | | 11.Björn Zikarsky | GER | 49.91s | 17. | | 12.Simon Brinn | JAM | 50.09s | 17. | | 13.Chris Fydler | AUS | 50.31s | 15. | | 14.Rostyslav Svanidze | UKR | 50.43s | 16. | | 15.Stephen Clarke | CAN | 50.45s | 11. | | 16.Bartosz Kizierowski | POL | 50.51s | 13. |
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| Heat 8 | Team | time | Rk. | | 1. Aleksandr Popov | RUS | 48.74s | 1. | | 2. Gustavo Borges | BRA | 49.17s | 3. | | 3. Fernando Scherer | BRA | 49.79s | 8. | | 4. Lars Frölander | SWE | 49.91s | 9. | | 5. Rostyslav Svanidze | UKR | 50.31s | 16. | | 6. Vladimir Predkin | RUS | 50.75s | 24. | | 7. Salim Iles | ALG | 50.87s | 25. | | 8. Nick Shackell | GBR | 51.03s | 28. |
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| Heat 7 | Team | time | Rk. | | 1. Stephen Clarke | CAN | 50.14s | 11. | | 2. Jon Olsen | USA | 50.17s | 12. | | 3. Chris Fydler | AUS | 50.27s | 15. | | 4. Björn Zikarsky | GER | 50.38s | 17. | | 5. Yoav Bruck | ISR | 50.61s | 22. | | 6. Nicolae Ivan | ROU | 51.14s | 30. | | 7. Béla Szabados | HUN | 51.26s | 35. | | 8. José Martín Meolans | ARG | 52.02s | 45. |
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| Heat 6 | Team | time | Rk. | | 1. Gary Hall, Jr. | USA | 48.90s | 2. | | 2. Francisco Sánchez | VEN | 49.59s | 4. | | 3. Pavlo Khnykin | UKR | 49.69s | 6. | | 4. Pieter van den Hoogenband | NED | 49.73s | 7. | | 5. Christian-Alexander Tröger | GER | 50.06s | 10. | | 6. Attila Zubor | HUN | 50.43s | 20. | | 7. Trent Bray | NZL | 51.18s | 31. | | 8. Richard Sam Bera | INA | 51.25s | 34. |
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| Heat 5 | Team | time | Rk. | | 1. Ricardo Busquets | PRO | 49.61s | 5. | | 2. Bartosz Kizierowski | POL | 50.18s | 13. | | 3. Oleg Rykhlevich | BLR | 50.42s | 19. | | 4. Aleksey Yegorov | KAZ | 50.49s | 21. | | 5. Nicolas Gruson | FRA | 50.71s | 23. | | 6. Brendon Dedekind | RSA | 50.95s | 26. | | 7. Earl McCarthy | IRE | 50.99s | 27. | | 8. Shunsuke Ito | JPN | 51.29s | 37. |
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| Heat 4 | Team | time | Rk. | | 1. Simon Brinn | JAM | 50.38s | 17. | | 2. Indrek Sei | EST | 51.19s | 32. | | 3. Juan Benavides | ESP | 51.20s | 33. | | 4. Felipe Delgado | ECU | 51.38s | 38. | | 5. Zhao Lifeng | CHN | 51.70s | 39. | | 6. Marijan Kanjer | CRO | 51.76s | 40. | | 7. Kalle Varonen | FIN | 52.00s | 44. | | 8. Tamer Hamed Zinhom | EGY | 52.16s | 47. |
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| Heat 3 | Team | time | Rk. | | 1. Sergey Ashikhmin | KGZ | 51.07s | 29. | | 2. Giovanni Linscheer | SUR | 51.82s | 41. | | 3. Li Kai Yien | HKG | 51.84s | 42. | | 4. José Isaza | PAN | 51.86s | 43. | | 5. Oleg Tsvetkovsky | UZB | 52.39s | 48. | | 6. Stavros Mikhailidis | CYP | 52.65s | 50. | | 7. Maxim Cazmirciuc | MDA | 53.18s | 55. | | 8. Huang Chih-Yung | TPE | 53.47s | 56. |
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| Heat 1 | Team | time | Rk. | | 1. Darrick Bollinger | GUM | 52.68s | 51. | | 2. Kenny Roberts | SEY | 52.89s | 52. | | 3. Diego Mularoni | SMR | 57.11s | 59. | | 4. Khuwaiter Al-Dhaheri | UAE | 57.70s | 60. |
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| Heat 2 | Team | time | Rk. | | 1. Raimundas Mažuolis | LTU | 50.27s | 14. | | 2. Janko Gojković | BIH | 51.28s | 36. | | 3. Georgios Giziotis | GRE | 52.04s | 46. | | 4. Go Un-Ho | KOR | 52.56s | 49. | | 5. Nikola Kalabić | YUG | 52.98s | 53. | | 6. Diego Perdomo | COL | 53.01s | 54. | | 7. Sng Ju Wei | SIN | 53.50s | 57. | | 8. Juan Luis Bocanegra | GUA | 54.05s | 58. |
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