1. Casey Stoner AUS Ducati Marlboro Team (B) 1min 32.968 secs
2. Sylvain Guintoli FRA Dunlop Yamaha Tech 3 (D) 1min 33.084 secs
3. Dani Pedrosa SPA Repsol Honda Team (M) 1min 33.150 secs
4. Marco Melandri ITA Honda Gresini (B) 1min 33.319 secs
5. Chris Vermeulen AUS Rizla Suzuki MotoGP (B) 1min 33.501 secs
6. Randy de Puniet FRA Kawasaki Racing Team (B) 1min 33.519 secs
7. Alex Barros BRA Pramac d'Antin (B) 1min 33.541 secs
8. Valentino Rossi ITA Fiat Yamaha Team (M) 1min 33.620 secs
9. Nicky Hayden USA Repsol Honda Team (M) 1min 33.650 secs
10. John Hopkins USA Rizla Suzuki MotoGP (B) 1min 33.680 secs
11. Carlos Checa SPA Honda LCR (M) 1min 33.831 secs
12. Makoto Tamada JPN Dunlop Yamaha Tech 3 (D) 1min 33.899 secs
13. Colin Edwards USA Fiat Yamaha Team (M) 1min 33.972 secs
14. Loris Capirossi ITA Ducati Marlboro Team (B) 1min 34.000 secs
15. Toni Elias SPA Honda Gresini (B) 1min 34.218 secs
16. Shinya Nakano JPN Konica Minolta Honda (M) 1min 34.352 secs
17. Anthony West AUS Kawasaki Racing Team (B) 1min 34.413 secs
18. Chaz Davies GBR Pramac d'Antin (B) 1min 35.029 secs *
19. Kurtis Roberts USA Team Roberts (M) 1min 35.335 secs

* time set in FP1.

2006 Valencian Grand Prix: Pole position: Valentino Rossi ITA Camel Yamaha (M) 1min 31.002secs Fastest race lap: Loris Capirossi ITA Ducati Marlboro (B) 1min 32.924secs