| Heat 6 | Team | time | Rk. | | 1. Ian Thorpe | AUS | 3:44.65 | 1. | | 2. Emiliano Brembilla | ITA | 3:48.41 | 4. | | 3. Klete Keller | USA | 3:48.62 | 6. | | 4. Nicolas Rostoucher | FRA | 3:51.80 | 12. | | 5. Aleksey Filipets | RUS | 3:52.21 | 14. | | 6. Rick Say | CAN | 3:52.72 | 15. | | 7. Mark Johnston | CAN | 3:54.99 | 21. | | 8. Ihor Chervynsky | UKR | 3:59.84 | 33. |
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| Heat 5 | Team | time | Rk. | | 1. Chade Carvin | USA | 3:48.42 | 5. | | 2. Dragoş Coman | ROU | 3:48.77 | 7. | | 3. Grant Hackett | AUS | 3:48.91 | 8. | | 4. Heiko Hell | GER | 3:50.80 | 9. | | 5. James Salter | GBR | 3:52.01 | 13. | | 6. Vlastimil Burda | CZE | 3:54.40 | 19. | | 7. Spyros Gianniotis | GRE | 3:54.96 | 20. | | 8. Ricardo Monasterio | VEN | 3:55.35 | 23. |
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