Calificación 250cc - Gran Premio de San Marino 2009
| Pos. | Piloto | Equipo | Moto | Tiempo |
|---|---|---|---|---|
| 1 | 
Hiroshi Aoyama |
Scot Racing Team | Honda | 1:38.867 |
| 2 | 
Héctor Barberá |
Pepe World Team | Aprilia | +0.008 |
| 3 | 
Marco Simoncelli |
Metis Gilera | Gilera | +0.171 |
| 4 |
Mattia Pasini |
Team Toth Aprilia | Aprilia | +0.201 |
| 5 | 
Mike Di Meglio |
+0.530 | ||
| 6 |
Alex Debón |
Aeropuerto-Castello-Blusens | Aprilia | +0.549 |
| 7 |
Héctor Faubel |
Thai Honda PTT SAG | Honda | +0.735 |
| 8 |
Alvaro Bautista |
Mapfre Aspar Team | Aprilia | +0.958 |
| 9 |
Roberto Locatelli |
Metis Gilera | Gilera | +1.048 |
| 10 | 
Ratthapark Wilairot |
Thai Honda PTT SAG | Honda | +1.102 |
| 11 | 
Karel Abraham |
Cardion AB Motoracing | Aprilia | +1.128 |
| 12 |
Lukas Pesek |
Auto Kelly - CP | Aprilia | +1.173 |
| 13 |
Jules Cluzel |
Matteoni Racing | Aprilia | +1.199 |
| 14 | 
Thomas Lüthi |
Emmi - Caffe Latte | Aprilia | +1.261 |
| 15 |
Alex Baldolini |
WTR San Marino Team | Aprilia | +1.269 |
| 16 |
Raffaele De Rosa |
Scot Racing Team | Honda | +1.965 |
| 17 |
Shoya Tomizawa |
CIP Moto | Honda | +2.562 |
| 18 |
Valentin Debise |
CIP Moto | Honda | +3.036 |
| 20 |
Axel Pons |
Pepe World Team | Aprilia | +3.291 |
| 21 |
Bastien Chesaux |
Racing Team Germany | Honda | +4.090 |
| 22 | 
Vladimir Leonov |
Viessmann Kiefer Racing | Aprilia | +4.125 |
| 23 | 
Imre Toth |
Team Toth Aprilia | Aprilia | +4.212 |
| 24 | 
Toby Markham |
C&L Racing | Honda | +5.052 |
| 25 |
Aitor Rodríguez |
Milar - Juegos Lucky | Aprilia | +6.490 |