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In this paper, a new method to determine repeatable runout (RRO) disturbance data is proposed. The obtained RRO disturbance data is further used to compensate for the RRO disturbance. The error transfer function (or sensitivity function) can be obtained without any additional instrument, and moreover the estimated RRO disturbance obtained from the proposed method will not be affected by the variation of the actuator model. Furthermore, the proposed method is much easier to be implemented than the fast Fourier transform and inverse fast Fourier transform (FFT/IFFT) method as much less computation is needed. Experimental results show that the servo tracking performance can be significantly improved by using the estimated disturbance to compensate the actual RRO disturbances. Comparative study between the proposed RRO compensation method and the iterative learning control (ILC)-based compensation method has also been performed in this paper.