In this paper, a new adaptive disturbance rejection scheme is introduced. In the proposed scheme, adaptive frequency estimation technique is incorporated into the traditional disturbance observer method. The frequency of the dominant disturbance is estimated online by a fast stable adaptive algorithm, and the estimated frequency is used to adaptively tune the bandwidth of the disturbance observer. Application to a HDD system shows that the proposed method exhibits good capability of disturbance rejection. Comparing with the traditional disturbance observer method, the new method incurs much less drop in phase margin.