Calificación 125cc - Gran Premio de San Marino 2009
| Pos. | Piloto | Equipo | Moto | Tiempo |
|---|---|---|---|---|
| 1 | 
Bradley Smith |
Bancaja Aspar Team | Aprilia | 1:43.727 |
| 2 | 
Julián Simón |
Bancaja Aspar Team | Aprilia | +0.016 |
| 3 | 
Andrea Iannone |
Ongetta Team I.S.P.A. | Aprilia | +0.163 |
| 4 |
Nicolás Terol |
Jack & Jones Team | Aprilia | +0.260 |
| 5 |
Sergio Gadea |
Bancaja Aspar Team | Aprilia | +0.335 |
| 6 |
Pol Espargaró |
Derbi Racing Team | Derbi | +0.444 |
| 7 |
Marc Márquez |
Red Bull KTM Motosport | KTM | +0.452 |
| 8 |
Simone Corsi |
Jack & Jones Team | Aprilia | +0.622 |
| 9 | 
Stefan Bradl |
Viessmann Kiefer Racing | Aprilia | +0.929 |
| 10 |
Sandro Cortese |
Ajo Interwetten | Derbi | +1.202 |
| 11 |
Efrén Vazquez |
Derbi Racing Team | Derbi | +1.389 |
| 12 |
Tito Rabat |
Blusens Aprilia | Aprilia | +1.430 |
| 13 |
Danny Webb |
Degraaf Grand Prix | Aprilia | +1.461 |
| 14 |
Scott Redding |
Blusens Aprilia | Aprilia | +1.486 |
| 15 | 
Johann Zarco |
WTR San Marino Team | Aprilia | +1.499 |
| 16 |
Luigi Morciano |
Junior GP Racing Dream | Aprilia | +1.589 |
| 17 | 
Michael Ranseder |
Haojue Team | Haojue | +1.723 |
| 18 |
Joan Olivé |
Derbi Racing Team | Derbi | +1.817 |
| 19 | 
Lukas Sembera |
WTR San Marino Team | Aprilia | +1.847 |
| 20 |
Lorenzo Zanetti |
Ongetta Team I.S.P.A. | Aprilia | +1.892 |
| 21 |
Alessandro Tonucci |
Junior GP Racing Dream | Aprilia | +1.960 |
| 22 | 
Takaaki Nakagami |
Ongetta Team I.S.P.A. | Aprilia | +2.049 |
| 23 | 
Randy Krummenacher |
Degraaf Grand Prix | Aprilia | +2.064 |
| 24 |
Dominique Aegerter |
Ajo Interwetten | Derbi | +2.068 |
| 25 |
Jonas Folger |
Ongetta Team I.S.P.A. | Aprilia | +2.141 |
| 26 |
Riccardo Moretti |
Elligi Racing | Aprilia | +2.205 |
| 27 |
Tomoyoshi Koyama |
Loncin Racing | Loncin | +2.221 |
| 28 | 
Cameron Beaubier |
Red Bull KTM Motosport | KTM | +2.244 |
| 29 |
Gabriele Ferro |
Grillini Bridgestone Team | Aprilia | +2.249 |
| 30 |
Lorenzo Savadori |
Fontana Racing | Aprilia | +2.603 |
| 31 |
Luis Salom |
SAG-Castrol | Honda | +2.625 |
| 32 |
Luca Marconi |
CBC Corse | Aprilia | +2.809 |
| 33 | 
Jasper Iwema |
WTR San Marino Team | Aprilia | +2.937 |
| 34 | 
Jacub Jantulik |
JJ Racing Team | Aprilia | +3.556 |
| 35 |
Jakub Kornfeil |
Loncin Racing | Loncin | +3.972 |
| 36 |
Luca Vitali |
CBC Corse | Aprilia | +4.287 |