In this paper, we describe a prototype system that. reconstructs three-dimensional (3D) blood vessels image from cone-beam projection images and analyzes the 3D reconstructed image. Several 3D reconstruction methods utilize biplane or stereo angiographic system and assume the cross section shapes of blood vessels (e.g. ellipse). However, the information provided by a few projections is insufficient for reconstructing a precise 3D image of blood vessels. Furthermore, the assumption of cross sectional shapes is not usually valid for abnormal blood vessels. In the present method using an X-ray rotational angiographic system, digital angiograms are collected in a short period time and a 3D image of blood vessels is approximately reconstructed using a short scan cone-beam reconstruction algorithm. The analysis method is based on the structure description of 3D blood vessels image. The procedure approximates the centerline of 3D blood vessels image using a 3D thinning algorithm and extracts the geometrical features of the 3D line pattern. Final graph data-structure is realized by the list representation with attributions representing geometrical features like edge points, branchings, and loops. From results of the application to patient’s cerebral blood vessels, we present the effectiveness of the system.