Abstract. This paper discusses the application of a set of computer graphics tools to the reconstruction of three-dimensional models from medical images. Specifically, this work is focused on in-vivo Magnetic Resonance Imaging (MRI) of the distal anastomosis of peripheral by-pass grafts. The aim of this study is the morphological classification of different anastomoses and the identification of correlations between shape, or more precisely a set of parameters representing shape, and blood flow patterns. Flows patterns are calculated using computational fluid dynamics (CFD) techniques on suitable computer representations of the reconstructed geometries. The reconstruction of a three-dimensional model of an anastomosis starts from a stack of planar sections of the lumen of the blood vessels produced by segmenting the MR images. An implicit function is fitted through the sections and it is chosen so that its zero-level contour is the interpolating surface of minimum curvature. A skeletonization algorithm extracts an approximation to the medial line of the threedimensional models. This medial line is used to determine the angles that blood vessels form at the anastomosis. The deviation of the medial line of the grafted vessel from the plane of the anastomosis yields a measure of planarity. These parameters allow a preliminary classification of shape. Scanning the same patient at different times postoperatively also allows to monitor changes in the shape of an anastomosis. Furthermore, scanning the same patient more than once, in different MRI scanners and at different resolutions constitutes an experimental validation of the reconstruction technique.