This paper is concerned with the design of discrete time sliding mode controller to sensorless flexible rotor-magnetic bearing systems (SFR-MBS). The plant dynamics, consisting of actuator dynamics and flexible rotor dynamics, are described. A variable structure system (VSS) disturbance observer, with which the state vector and disturbance can be estimated simultaneously, is investigated to compensate the mismatched disturbance. A new discrete time sliding mode servo controller, which can attenuate the chattering phenomenon, is proposed by using this VSS observer. The usefulness of the proposed controller is demonstrated through the computer simulations for a sensorless flexible rotor-magnetic bearing system under external disturbances and modeling uncertainties.