Since a repetitive control system can track a periodic reference input and reject a periodic disturbance perfectly, it has been widely applied in control engineering practice. However, the disturbance-rejection performance is not satisfactory for a non-periodic disturbance or for a periodic disturbance with a period different from that of the repetitive controller. To solve this problem, this paper presents a new configuration of a repetitive control system that incorporates an equivalent-input-disturbance estimator. A sufficient stability criterion is derived based on the separation and small gain theorems. A design algorithm is developed for the system based on the stability criterion. Simulation results of a disk drive servo system are used to verify the effectiveness of the method.