Ultrasonic imaging using complementary coded pulses offers the SNR improvements of signal coding without the filter side-lobes introduced by single-transmit codes. Tissue motion between coded pulse emissions, however, can introduce high side-lobes caused by misalignment of complementary filter outputs. This paper presents a method for filtering and motion compensation of complementary coded signals appropriate for use in medical imaging. The method is robust to the effects of non-ideal transducers on the imaging signals, includes mirrored compensation stages to reduce the impact of motion estimation error, and has been shown to reduce side-lobes to levels that compare favorably to systems using FM-coded signals of similar length and bandwidth while providing increased coding gain and range resolution. In addition, motion compensation allows the received data to be used without the frame-rate penalty usually incurred by complementary-coded imaging. The method has been verified using simulated point and speckle targets with both homogeneous and inhomogeneous motion profiles. Selected results have been verified experimentally.