The circuit was soaking wet during warm-up with rain still falling.
Randy de Puniet and then Valentino Rossi both walked away from lowside falls under braking for the final chicane.
Monster Yamaha Tech 3's Colin Edwards is making his comeback from a broken collarbone, but team-mate Cal Crutchlow will miss his home race after breaking his collarbone in qualifying.
Repsol Honda's Dani Pedrosa, who suffered a similar injury at Le Mans last month, is also absent from today's race.
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1. Casey Stoner
AUS Repsol Honda Team 2m 19.071s
2. Jorge Lorenzo
ESP Yamaha Factory Racing 2m 19.499s
3. Marco Simoncelli
ITA San Carlo Honda Gresini 2m 20.599s
4. Ben Spies
USA Yamaha Factory Racing 2m 21.672s
5. Andrea Dovizioso
ITA Repsol Honda Team 2m 21.700s
6. Alvaro Bautista
ESP Rizla Suzuki MotoGP 2m 23.564s
7. Karel Abraham
CZE Cardion AB Motoracing 2m 24.029s
8. Valentino Rossi
ITA Ducati Marlboro Team 2m 24.497s
9. Nicky Hayden
USA Ducati Marlboro Team 2m 24.715s
10. Toni Elias
ESP LCR Honda MotoGP 2m 26.723s
11. Hector Barbera
ESP Mapfre Aspar Team 2m 27.112s
12. Colin Edwards
USA Monster Yamaha Tech 3 2m 27.224s
13. Loris Capirossi
ITA Pramac Racing Team 2m 27.471s
14. Hiroshi Aoyama
JPN San Carlo Honda Gresini 2m 29.370s
15. Randy de Puniet
FRA Pramac Racing Team 2m 33.807s
AUS Repsol Honda 2m 2.020s
2010 British Grand Prix (June 20):
ESP Fiat Yamaha 2m 3.308s
Fastest race lap:
ESP Fiat Yamaha 2m 3.526s