A method for reducing motion artifacts in optical coherence tomography (OCT) angiography images is disclosed. The method is applied to the intensity or complex OCT data prior to applying the motion contrast analysis and involves determining sub-pixel level shifts between at least two B-scans repeated approximately at the same location and applying the sub-pixel level shifts to the B-scans to be able to correct for motion and accurately determine motion contrast signal. A preferred embodiment includes the use of 2D cross correlations to register a series of B-scans in both the axial (z-) and lateral (x-) dimensions and a convolution approach to achieve sub-pixel level frame registration.