| # | Rider | Team | Time | Gap |
|---|---|---|---|---|
| 1 | Damiano Cunego | Lampre | 04:04:57 | |
| 2 | Giovanni Visconti | Quick Step | + 00 | |
| 3 | Ivan Basso | Liquigas | + 00 | |
| 4 | Valerio Agnoli | Liquigas | + 12 | + 12 |
| 5 | Francesco Gavazzi | Lampre | + 01:23 | + 01:23 |
| 6 | Thomas Voeckler | Bouygues Telecom | + 01:23 | + 01:23 |
| 7 | Kjell Carlström | Liquigas | + 01:23 | + 01:23 |
| 8 | Alessandro Proni | Quick Step | + 01:23 | + 01:23 |
| 9 | Yukihiro Doi | Skil - Shimano | + 01:23 | + 01:23 |
| 10 | Taiji Nishitani | Aisan Racing Team | + 01:23 | + 01:23 |
| 11 | Paolo Tiralongo | Lampre | + 01:29 | + 01:29 |
| 12 | Gorazd Stangelj | Liquigas | + 01:30 | + 01:30 |
| 13 | Yukiya Arashiro | Meitan Hompo - GDR | + 01:35 | + 01:35 |
| 14 | Marco Marzano | Lampre | + 01:51 | + 01:51 |
| 15 | Shinri Suzuki | Skil - Shimano | + 03:33 | + 03:33 |
| 16 | Alex Coutts | Giant Asia Racing Team | + 03:35 | + 03:35 |
| 17 | Kazuo Inoue | Nippo - Endeka | + 03:40 | + 03:40 |
| 18 | Junya Sano | Nippo - Endeka | + 03:46 | + 03:46 |
| 19 | Erik Hoffmann | Giant Asia Racing Team | + 03:46 | + 03:46 |
| 20 | Kazuhiro Mori | Aisan Racing Team | + 03:50 | + 03:50 |
| 21 | Masahiro Shinagawa | Aisan Racing Team | + 03:50 | + 03:50 |
| 22 | Miyataka Shimizu | Meitan Hompo - GDR | + 03:50 | + 03:50 |
| 23 | Shimpei Fukuda | Team Bridgestone - Anchor | + 04:44 | + 04:44 |
| 24 | Takahiro Yamashita | Nippo - Endeka | + 04:44 | + 04:44 |
| 25 | Hidenori Nodera | Skil - Shimano | + 04:44 | + 04:44 |
| 26 | Rhys Pollock | Trek - Marco Polo | + 04:44 | + 04:44 |
| 27 | Masakazu Ito | + 04:44 | + 04:44 | |
| 28 | Yoshiyuki Shimizu | Nippo - Endeka | + 04:44 | + 04:44 |
| 29 | Olivier Bonnaire | Bouygues Telecom | + 04:44 | + 04:44 |
| 30 | Kazuya Okazaki | Meitan Hompo - GDR | + 04:44 | + 04:44 |
| 31 | Hayato Yoshida | + 04:44 | + 04:44 | |
| 32 | Jai Crawford | Trek - Marco Polo | + 04:44 | + 04:44 |
| 33 | Kazuyuki Manabe | Nippo - Endeka | + 04:44 | + 04:44 |
| 34 | Kazuki Aoyanagi | + 04:44 | + 04:44 | |
| 35 | Tomoya Kano | Skil - Shimano | + 04:44 | + 04:44 |
| 36 | Naoki Mukaigawa | Matrix Powertag - Corratec | + 04:44 | + 04:44 |
| 37 | Yoshimitsu Hiratsuka | + 04:48 | + 04:48 | |
| 38 | Fuyu Li | Trek - Marco Polo | + 04:48 | + 04:48 |
| 39 | Mauro Facci | Quick Step | + 04:48 | + 04:48 |
| 40 | Yasuharu Nakajima | Meitan Hompo - GDR | + 04:49 | + 04:49 |
| 41 | Vladimir Miholjevic | Liquigas | + 04:49 | + 04:49 |
| 42 | Takeaki Ayabe | Aisan Racing Team | + 04:49 | + 04:49 |
| 43 | Masaru Fukuhara | Team Bridgestone - Anchor | + 04:55 | + 04:55 |
| 44 | Perrig Quemeneur | Bouygues Telecom | + 09:33 | + 09:33 |
| 45 | Leonardo Scarselli | Quick Step | + 09:33 | + 09:33 |
| 46 | David Mccann | Giant Asia Racing Team | + 09:33 | + 09:33 |
| 47 | Yohann Gène | Bouygues Telecom | + 09:33 | + 09:33 |
| 48 | Marco Bandiera | Lampre | + 09:33 | + 09:33 |
| 49 | Stijn Joseph | Quick Step | + 09:33 | + 09:33 |
| 50 | Masahiko Mifune | Matrix Powertag - Corratec | + 09:39 | + 09:39 |
| 51 | Masamichi Yamamoto | Team Bridgestone - Anchor | + 11:24 | + 11:24 |