There is disclosed a system and method for diagnosing plagiocephaly (flat head syndrome, associated primarily with in infants) from photographs of the head. The method and apparatus may involve the use of a processor circuit, for example an application server, for automatically identifying the contour of the head in a plurality of images, then computing geometrical measurements in order quantify plagiocephaly. Photographs are acquired from an overhead view of a head, where the images may be rotated manually or automatically to a standard orientation. For each image, an optimal head contour is identified as minimizing a mathematical cost function combining local image filter responses designed for edge detection and a global model of head contour shape combining smoothness and convexity constrains. Length measurements are then computed from the identified contour, e.g. head diameter, diagonal diameter, and used to quantify the degree of head asymmetry and diagnose plagiocephaly.