| Ranking | time | | React. | BY |
| 1. Pieter Van Den Hoogenband | NED | 48.96s | | 0.82 | 78 |
| 2. Anthony Ervin | USA | 49.08s | | 0.68 | 81 |
| 3. Ian Thorpe | AUS | 49.21s | | 0.81 | 82 |
| 4. Torsten Spanneberg | GER | 49.40s | | 0.83 | 75 |
| 5. Ashley Callus | AUS | 49.46s | | 0.74 | 79 |
| 6. Jason Lezak | USA | 49.51s | | 0.73 | 75 |
| 7. Stefan Nystrand | SWE | 49.65s | | 0.76 | 81 |
| 7. Jose Martin Meolans | ARG | 49.65s | | 0.80 | 78 |
| 9. Attila Zubor | HUN | 49.73s | | 0.82 | 75 |
| 10.Lars Frolander | SWE | 49.76s | | 0.75 | 74 |
| 11.Salim Iles | ALG | 49.80s | | 0.71 | 75 |
| 11.Gustavo Borges | BRA | 49.80s | | 0.73 | 72 |
| 13.Lars Conrad | GER | 49.89s | | 0.83 | 76 |
| 14.Duje Draganja | CRO | 49.90s | | 0.81 | 83 |
| 15.Edvaldo Silva Filho | BRA | 50.03s | | 0.67 | 78 |
| 16.Johan Kenkhuis | NED | 50.08s | | 0.78 | 80 |
| eliminated |
| 17.Roland Schoeman | RSA | 50.13s | | 0.70 | 00 |
| 17.Bartosz Kizierowski | POL | 50.13s | | 0.71 | 77 |
| 19.Vyacheslav Shyrshov | UKR | 50.22s | | 0.78 | 79 |
| 20.Karel Novy | SUI | 50.25s | | 0.84 | 80 |
| 21.Simone Cercato | ITA | 50.41s | | 0.79 | 75 |
| 22.Rolandas Gimbutis | LTU | 50.65s | | 0.82 | 81 |
| 23.Nicholas Folker | RSA | 50.66s | | 0.68 | 76 |
| 24.Ivan Mladina | CRO | 50.73s | | 0.77 | 80 |
| 25.Jorge Ulibarri | ESP | 50.76s | | 0.76 | 75 |
| 26.Yoshihiro Okumura | JPN | 50.91s | | 0.72 | 83 |
| 27.Riley Janes | CAN | 51.19s | | 0.72 | 80 |
| 28.Shunsuke Ito | JPN | 51.29s | | 0.68 | 76 |
| 29.Maxim Korchounov | RUS | 51.40s | | 0.93 | 77 |
| 30.Oleksandr Volynets | UKR | 51.52s | | 0.80 | 74 |
| 31.Oswaldo Quevedo | VEN | 51.63s | | 0.69 | 76 |
| 32.Min suk Kim | KOR | 51.71s | | 0.76 | 79 |
| 33.Danil Haustov | EST | 51.78s | | 0.78 | 80 |
| 34.Xufeng Xie | CHN | 51.81s | | 0.82 | 78 |
| 35.Christoph Buhler | SUI | 51.87s | | 0.77 | 74 |
| 36.Kunpeng Ouyang | CHN | 51.88s | | 0.75 | 82 |
| 37.Saulius Binevicius | LTU | 51.97s | | 0.90 | 79 |
| 38.Carl Probert | FIJ | 52.15s | | 0.83 | 75 |
| 39.Alejandro Siqueiros | MEX | 52.30s | | 0.74 | 82 |
| 40.Camilo Becerra | COL | 52.41s | | 0.82 | 80 |
| 41.Nien-pin Wu | TPE | 52.70s | | 0.58 | 83 |
| 42.Mark Chay | SIN | 52.77s | | 0.74 | 82 |
| 43.Ismael Ortiz | PAN | 52.93s | | 0.79 | 82 |
| 44.Brendan Ashby | ZIM | 53.14s | | 0.67 | 80 |
| 45.Gustavo Barrios | PAN | 53.34s | | 0.79 | 78 |
| 46.Ernest Teo | SIN | 53.39s | | 0.77 | 76 |
| 47.Christophe Lim Wen Ying | MRI | 53.64s | | 0.73 | 81 |
| 48.Jacob Fraire | MEX | 53.76s | | 0.79 | 80 |
| 49.Wing harbeth Fu | HKG | 53.79s | | 0.75 | 80 |
| 50.Victor Rogut | MDA | 53.93s | | 0.84 | 79 |
| 51.Chon Kit Alias Joao Tang | MAC | 53.94s | | 0.82 | 79 |
| 52.Gregory Arkhurst | CIV | 54.01s | | 0.69 | |
| 53.Christophee Backisavs | DOM | 54.05s | | 0.85 | 85 |
| 54.Ronald Cowen | BER | 54.65s | | 0.71 | 80 |
| 55.Nicholas Diaper | KEN | 54.71s | | 0.70 | 80 |
| 56.Kenny Roberts | SEY | 54.76s | | 0.77 | 78 |
| 57.Cliff Gittens | BAR | 54.96s | | 0.74 | 83 |
| 58.Vakhtang Beridze | GEO | 54.99s | | 0.72 | 80 |
| 59.Bing-ru Jiang | TPE | 55.03s | | 0.79 | |
| 60.Ahmed Obaid S Obaid Al Jassimi | UAE | 55.05s | | 0.82 | 81 |
| 61.Saad Khalloqi | MAR | 55.08s | | 0.87 | 78 |
| 62.Khuwiater Saeed Had Al Dhaheri | UAE | 55.15s | | 0.69 | 79 |
| 63.Gael Souci | MRI | 55.21s | | 0.73 | 84 |
| 64.Khaly Ciss | SEN | 55.25s | | 0.83 | 81 |
| 65.Davy Rolando Bisslik | ARU | 55.32s | | 0.76 | 82 |
| 66.Aleksey Bortnikov | UZB | 55.56s | | 0.82 | 83 |
| 67.Barnsley Albert | SEY | 55.91s | | 0.88 | 74 |
| 68.Arwut Chinnapasaen | THA | 55.92s | | 0.78 | 80 |
| 69.Wing Cheung Victor Wong | MAC | 56.24s | | 0.76 | 84 |
| 70.Omar Nunez | NCA | 56.75s | | 0.84 | 83 |
| 71.Yu-lung Lubrey Lim | MAS | 57.23s | | 0.90 | 82 |
| 72.Zie Ahmed Oyattara | CIV | 57.44s | | 0.86 | 81 |
| 73.Onan Thom | GUY | 57.56s | | 0.72 | 84 |
| 74.Hamid Nassir | KEN | 57.68s | | 0.71 | 84 |
| 75.Rainui Teriipaia | TAH | 57.69s | | 0.81 | 00 |
| 76.Joao Carlos da S.Paquet Aguiar | ANG | 57.76s | | 0.75 | 83 |
| 77.Seung gin Lee | NMA | 57.83s | | 0.73 | 85 |
| 78.Mark Unpingco | GUM | 58.33s | | 0.76 | 83 |
| 79.William Kang | GUM | 58.36s | | 0.78 | 85 |
| 80.Ganaa Galbadrakh | MGL | 58.49s | | 0.80 | 74 |
| 81.Nuno Miguel Cardoso Rola | ANG | 58.51s | | 0.78 | 83 |
| 82.Dean Palacios | NMA | 58.77s | | 0.68 | 86 |
| 83.Sule Cole Shade | CMR | 1:01.70 | | 0.75 | 80 |
| 84.Rony Bakale | CGO | 1:02.38 | | 0.88 | 87 |
| 85.Joe Atuhairwe | UGA | 1:07.71 | | 0.85 | 78 |
| 86.Ibrahim Ismael Mamadou | NIG | 1:11.78 | | 1.18 | 80 |
| 87.Fabrice Ndikumana | BDI | 1:15.05 | | 1.31 | 83 |
| 88.Joshua Robert Marfleet | SAM | 1:29.41 | | 0.98 | 87 |
| -. Eithan Urbach | ISR | DNS | | | 77 |
| -. Hesham Shehab | BRN | DNS | | | 88 |
| -. Richard sam Bera | INA | DNS | | | 71 |
| -. George Bovell | TRI | DNS | | | 83 |
| -. Lorenzo Vismara | ITA | DNS | | | 75 |
| -. Peter Mankoc | SLO | DNS | | | 78 |