Methods of compensating for repeatable runout in a disk drive are provided. The disk drive includes a data storage disk, a transducer adjacent to the disk, a primary actuator for positioning the transducer over a first range of movement, and a secondary actuator for positioning the transducer over a second range of movement that is less than the first range of movement. Estimates are made of the position of the secondary actuator in the second range of movement. Data is read from the disk via the transducer. A position error signal is determined based on the read data. Positioning of the transducer by the primary actuator is controlled based on the estimated position of the secondary actuator in the second range of movement and based on the position error signal to compensate for repeatable runout.