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Date: 18 August 2004
Summary
Final 1
| Rank | Name | Nation | Time |
| 1 | Pieter van den Hoogenband | NED | 48.17 |
| 2 | Roland Schoeman | RSA | 48.23 |
| 3 | Ian Thorpe | AUS | 48.56 |
| 4 | Ryk Neethling | RSA | 48.63 |
| 5 | Filippo Magnini | ITA | 48.99 |
| 6 | Duje Draganja | CRO | 49.23 |
| 7 | Salim Iles | ALG | 49.30 |
| 7 | Andrey Kapralov | RUS | 49.30 |