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| 1 | FIAT Yamaha Team | 617 | 45 | 41 | 45 | 20 | 25 | 25 | 26 | 33 | 41 | 36 | 29 | 36 | 23 | 29 | 41 | 36 | 45 | 41 |
| 2 | Repsol Honda Team | 451 | 25 | 30 | 27 | 41 | 28 | 31 | 22 | 36 | 13 | 20 | 36 | 38 | 20 | 20 | 20 | – | 24 | 20 |
| 3 | Ducati Marlboro Team | 388 | 13 | 24 | 13 | 13 | 24 | 25 | 24 | 25 | 31 | 26 | 10 | 11 | 41 | 29 | 10 | 38 | 11 | 20 |
| 4 | Monster Yamaha Tech 3 | 279 | 19 | 4 | 4 | 12 | 23 | 21 | 15 | 8 | 19 | 22 | 20 | 19 | 15 | 19 | 13 | 20 | 9 | 17 |
| 5 | San Carlo Honda Gresini | 228 | 8 | 13 | 16 | 18 | 9 | 7 | 7 | 16 | 8 | 13 | 9 | 8 | 16 | 15 | 15 | 17 | 20 | 13 |
| 6 | Rizla Suzuki | 129 | 7 | 6 | – | 8 | 4 | 5 | 20 | 5 | 6 | – | 13 | 8 | 8 | 9 | 11 | 4 | 8 | 7 |
| 7 | LCR Honda MotoGP | 121 | 10 | 7 | 9 | 10 | 10 | 10 | 13 | – | 5 | 6 | 3 | 3 | – | 7 | 6 | 6 | 10 | 6 |
| 8 | Pramac Racing Team | 109 | – | 10 | 10 | 8 | 9 | 11 | 4 | – | 7 | 4 | 7 | 5 | 8 | 3 | 4 | 13 | – | 6 |
| 9 | Páginas Amarillas Aspar MotoGP Team | 90 | 4 | 3 | 8 | 4 | 5 | 4 | 6 | 7 | – | 7 | 6 | 7 | 5 | 3 | 5 | 2 | 6 | 8 |
| 10 | Interwetten Honda MotoGP | 68 | 6 | 2 | 5 | 5 | – | 1 | 3 | 4 | 4 | 3 | 4 | 4 | 3 | 6 | 9 | 3 | 4 | 2 |
