Active magnetic bearings have several advantages over conventional mechanical and fluid bearings. However, when the magnetic bearings are used at high rotational speeds, whirling motions and vibrations synchronized with the rotation of the rotor should be considered. In order to suppress these unfavorable vibrations of rotor which is supported by magnetic bearings, we have developed an active vibration control system with a two-level control structure. Experimental results show that our active bearings system effectively suppresses the whirling motion.