| # | Rider | Team | Time | Gap |
|---|---|---|---|---|
| 1 | Damiano Cunego | Lampre-Caffita | 04:05:56 | |
| 2 | Francisco Mancebo | Illes Balears - Caisse d'Epargne | + 03 | + 03 |
| 3 | Cristian Moreni | Quick Step | + 27 | + 27 |
| 4 | Pablo Lastras | Illes Balears - Caisse d'Epargne | + 43 | + 43 |
| 5 | Manuele Mori | Saunier Duval - Prodir | + 43 | + 43 |
| 6 | Patrik Sinkewitz | Quick Step | + 44 | + 44 |
| 7 | Yasutaka Tashiro | Team Bridgestone - Anchor | + 51 | + 51 |
| 8 | Morris Possoni | Lampre-Caffita | + 01:51 | + 01:51 |
| 9 | Shinri Suzuki | Team Bridgestone - Anchor | + 01:51 | + 01:51 |
| 10 | Kam-po Wong | + 01:52 | + 01:52 | |
| 11 | Marco Marzano | Lampre-Caffita | + 01:52 | + 01:52 |
| 12 | Makoto Iijima | Sumita Ravanello Pearlizumi | + 01:52 | + 01:52 |
| 13 | Vicente García José | Illes Balears - Caisse d'Epargne | + 01:52 | + 01:52 |
| 14 | Kazuyuki Manabe | Team Nippo | + 01:53 | + 01:53 |
| 15 | Kazuya Okazaki | Team Nippo | + 01:53 | + 01:53 |
| 16 | San Wu Kin | + 01:53 | + 01:53 | |
| 17 | Patxi Vila | Lampre-Caffita | + 01:54 | + 01:54 |
| 18 | Hidenori Nodera | Shimano - Memory Corp | + 01:54 | + 01:54 |
| 19 | Kazuhiro Mori | + 01:55 | + 01:55 | |
| 20 | Yukihiro Doi | Shimano - Memory Corp | + 02:01 | + 02:01 |
| 21 | Tomoya Kano | Shimano - Memory Corp | + 02:18 | + 02:18 |
| 22 | Joan Horrach | Illes Balears - Caisse d'Epargne | + 02:21 | + 02:21 |
| 23 | Taiji Nishitani | + 02:33 | + 02:33 | |
| 24 | Yusuke Shimizu | Team Bridgestone - Anchor | + 03:09 | + 03:09 |
| 25 | José Gomez | Saunier Duval - Prodir | + 03:42 | + 03:42 |
| 26 | Manuel Quinziato | Saunier Duval - Prodir | + 03:42 | + 03:42 |
| 27 | Ken Hashikawa | Kinan CCD | + 06:37 | + 06:37 |
| 28 | Koji Fukushima | Team Bridgestone - Anchor | + 06:38 | + 06:38 |
| 29 | Masahiro Shinagawa | Shimano - Memory Corp | + 06:38 | + 06:38 |
| 30 | Yoshimasa Hirose | Shimano - Memory Corp | + 06:38 | + 06:38 |
| 31 | Mikel Pradera | Illes Balears - Caisse d'Epargne | + 06:39 | + 06:39 |
| 32 | Alessandro Ballan | Lampre-Caffita | + 06:41 | + 06:41 |
| 33 | Hing Chan Chun | + 09:20 | + 09:20 | |
| 34 | Akira Kakinuma | Miyata - Subaru Racing Team | + 09:26 | + 09:26 |
| 35 | Kojiro Nakagawa | Miyata - Subaru Racing Team | + 09:26 | + 09:26 |
| 36 | Davide Bramati | Quick Step | + 09:26 | + 09:26 |
| 37 | Ivan Santaromita | Quick Step | + 09:27 | + 09:27 |
| 38 | Ching Wong Ngai | + 09:27 | + 09:27 | |
| 39 | Kevin Hulsmans | Quick Step | + 09:28 | + 09:28 |
| 40 | Takumi Beppu | + 09:28 | + 09:28 | |
| 41 | Masahiko Mifune | Miyata - Subaru Racing Team | + 09:28 | + 09:28 |
| 42 | Ruben Lobato | Saunier Duval - Prodir | + 12:14 | + 12:14 |