Calificación 250cc - Gran Premio de Malasia 2009
| Pos. | Piloto | Equipo | Moto | Tiempo |
|---|---|---|---|---|
| 1 | 
Hiroshi Aoyama |
Scot Racing Team | Honda | 2:06.767 |
| 2 | 
Jules Cluzel |
Matteoni Racing | Aprilia | +0.332 |
| 3 |
Mike Di Meglio |
+0.465 | ||
| 4 | 
Héctor Barberá |
Pepe World Team | Aprilia | +0.534 |
| 5 |
Alvaro Bautista |
Mapfre Aspar Team | Aprilia | +0.604 |
| 6 | 
Ratthapark Wilairot |
Thai Honda PTT SAG | Honda | +0.895 |
| 7 |
Héctor Faubel |
Thai Honda PTT SAG | Honda | +1.061 |
| 8 | 
Marco Simoncelli |
Metis Gilera | Gilera | +1.149 |
| 9 | 
Thomas Lüthi |
Emmi - Caffe Latte | Aprilia | +1.182 |
| 10 |
Raffaele De Rosa |
Scot Racing Team | Honda | +1.186 |
| 11 |
Alex Debón |
Aeropuerto-Castello-Blusens | Aprilia | +1.231 |
| 12 |
Mattia Pasini |
Team Toth Aprilia | Aprilia | +1.392 |
| 13 |
Roberto Locatelli |
Metis Gilera | Gilera | +2.069 |
| 14 |
Alex Baldolini |
WTR San Marino Team | Aprilia | +2.074 |
| 15 | 
Karel Abraham |
Cardion AB Motoracing | Aprilia | +2.141 |
| 16 |
Shoya Tomizawa |
CIP Moto | Honda | +2.381 |
| 17 |
Lukas Pesek |
Auto Kelly - CP | Aprilia | +2.569 |
| 18 |
Axel Pons |
Pepe World Team | Aprilia | +2.625 |
| 19 |
Shuhei Aoyama |
Racing Team Germany | Honda | +2.887 |
| 21 |
Bastien Chesaux |
Racing Team Germany | Honda | +5.174 |
| 22 |
Valentin Debise |
CIP Moto | Honda | +5.404 |
| 23 | 
Vladimir Leonov |
Viessmann Kiefer Racing | Aprilia | +6.046 |
| 24 | 
Imre Toth |
Team Toth Aprilia | Aprilia | +8.064 |