An algorithm is described which provides necessary information for automated registration and computation of alveolar height for subtraction radiographic analysis. This procedure involves identification of the cemento-enamel junctions from radiographic images by incrementally comparing a characteristic image signature along computed tooth boundaries. The identification of these anatomically invariant structures provides information necessary to warp images and create automatic superimposition, correcting for geometric misalignment. The present report describes and demonstrates the feasibility of utilizing automated CEJ, edge finding and image warping algorithms to align automatically sequential radiographs and permit their subtraction.