A motion compensated digitally subtracted Angiography (DSA) image processing system includes an interface for acquiring a sequence of images of patient vessels both prior to and following introduction of contrast agent into the vessels. An image data processor automatically, (a) determines a first shift vector for a first image of the sequence for compensating for shift between the first image and a first reference image of the sequence, (b) applies the determined first shift vector to the first image of the sequence to produce a shifted image, (c) subtracts the first reference image from the shifted image to produce a subtracted image enhancing vessel structure, (d) determines a second shift vector for compensating for shift between the subtracted image and a second reference image and (e) shifts content of the subtracted image relative to the second reference image in response to the second shift vector, to provide a shifted subtracted image enhancing and aligning vessel structure.