In order to minimize vibration problems of rotating machinery rotors have been assembled through balancing machines. Since perfect balancing is impossible, residual unbalances cause serious vibration while the rotor is in high speed region. To minimize unbalance effects of magnetic bearing systems (AMB) during rotation on-line balancing methodology was studied. Unbalances were considered as disturbances of the system. The disturbance observer was used to estimate unbalance force from measurable state and input variables. Balancing inputs computed according to LQR and outputs of the observer were applied to eliminate unbalances during high speed rotation of the AMB. the effectiveness of the on-line balancing was verified through numerical simulations.