| # | Rider | Team | Time | Gap |
|---|---|---|---|---|
| 1 | Anker Sørensen Chris | Team Saxo Bank | 04:06:19 | |
| 2 | Daniel Moreno | Caisse d'Epargne | + 24 | + 24 |
| 3 | Ivan Santaromita | Liquigas | + 24 | + 24 |
| 4 | José Cobo Juan | Fuji-Servetto | + 24 | + 24 |
| 5 | Pablo Lastras | Caisse d'Epargne | + 41 | + 41 |
| 6 | Joaquim Rodríguez | Caisse d'Epargne | + 01:00 | + 01:00 |
| 7 | Valerio Agnoli | Liquigas | + 01:26 | + 01:26 |
| 8 | Giovanni Visconti | ISD - Neri | + 01:26 | + 01:26 |
| 9 | Shinri Suzuki | Shimano Racing Team | + 02:09 | + 02:09 |
| 10 | Gustav Larsson | Team Saxo Bank | + 02:09 | + 02:09 |
| 11 | Johann Tschopp | BBOX Bouygues Telecom | + 02:09 | + 02:09 |
| 12 | Taiji Nishitani | Aisan Racing Team | + 02:21 | + 02:21 |
| 13 | Takashi Miyazawa | EQA - Meitan Hompo - GDR | + 02:21 | + 02:21 |
| 14 | Makoto Iijima | Team Bridgestone - Anchor | + 02:21 | + 02:21 |
| 15 | Miyataka Shimizu | EQA - Meitan Hompo - GDR | + 02:21 | + 02:21 |
| 16 | Masahiro Shinagawa | Aisan Racing Team | + 02:24 | + 02:24 |
| 17 | David de La Fuente | Fuji-Servetto | + 02:24 | + 02:24 |
| 18 | Shinichi Fukushima | EQA - Meitan Hompo - GDR | + 03:01 | + 03:01 |
| 19 | Hidenori Nodera | Shimano Racing Team | + 03:01 | + 03:01 |
| 20 | Yukihiro Doi | + 03:01 | + 03:01 | |
| 21 | Kenji Itami | Team Bridgestone - Anchor | + 03:01 | + 03:01 |
| 22 | Tomoya Kano | Shimano Racing Team | + 03:05 | + 03:05 |
| 23 | Kjell Carlström | Liquigas | + 03:21 | + 03:21 |
| 24 | Ivan Basso | Liquigas | + 03:21 | + 03:21 |
| 25 | Alessandro Proni | ISD - Neri | + 03:21 | + 03:21 |
| 26 | Fredrik Kessiakoff | Fuji-Servetto | + 03:21 | + 03:21 |
| 27 | Imanol Erviti | Caisse d'Epargne | + 03:21 | + 03:21 |
| 28 | Yukiya Arashiro | BBOX Bouygues Telecom | + 03:25 | + 03:25 |
| 29 | Yasuharu Nakajima | EQA - Meitan Hompo - GDR | + 04:34 | + 04:34 |
| 30 | Kazuhiro Mori | Aisan Racing Team | + 04:38 | + 04:38 |
| 31 | Jens Voigt | Team Saxo Bank | + 05:13 | + 05:13 |
| 32 | Takayuki Naganuma | Blitzen Utsunomiya | + 05:17 | + 05:17 |
| 33 | Kenichi Suzuki | Aisan Racing Team | + 05:22 | + 05:22 |
| 34 | Masaru Fukuhara | Team Bridgestone - Anchor | + 07:59 | + 07:59 |
| 35 | Yoshimitsu Hiratsuka | + 08:49 | + 08:49 | |
| 36 | Andrea Tonti | Fuji-Servetto | + 12:12 | + 12:12 |
| 37 | Gianluca Mirenda | ISD - Neri | + 12:12 | + 12:12 |
| 38 | Yusuke Hatanaka | Shimano Racing Team | + 12:12 | + 12:12 |
| 39 | Guillaume Le Floch | BBOX Bouygues Telecom | + 12:12 | + 12:12 |
| 40 | Masaki Wakumoto | Matrix Powertag | + 12:12 | + 12:12 |
| 41 | Ryohei Komori | + 12:12 | + 12:12 | |
| 42 | Nicki Sørensen | Team Saxo Bank | + 12:12 | + 12:12 |
| 43 | Julien Guay | BBOX Bouygues Telecom | + 12:12 | + 12:12 |
| 44 | Yoshiyuki Shimizu | Blitzen Utsunomiya | + 12:12 | + 12:12 |
| 45 | Masaaki Kikuchi | EQA - Meitan Hompo - GDR | + 12:12 | + 12:12 |
| 46 | Kensho Sawada | Matrix Powertag | + 12:12 | + 12:12 |
| 47 | Kazuki Aoyanagi | + 12:12 | + 12:12 | |
| 48 | Ryota Nishizono | + 12:12 | + 12:12 |