In this paper we investigate the vibration characteristics of a rotor system with flexible disks. The coupled vibration mode between rotating shaft and the flexible disk are analyzed for lateral and axial vibrations respectively. Gyro and sheer effects are considered for the modeling of lateral vibrations. An assumed mode method was used for the disk modeling considering gyro effects. For a numerical example hard disk drive is considered. The natural frequencies of the motor-spindle system with flexible disk of hard disk drive was calculated and compared to the experimental data.