Over the past few years, very little has been done in the area of 3-D reconstruction of the bile duct. Since the system in use for 3-D visualization of the biliary tree is built by surgical or autopsy materials, it generally cannot be applied to clinical diagnosis. In this paper, an algorithm for three-dimensional reconstruction of the biliary tree from two mutually orthogonal is presented to provide accurate and reproducible 3-D information of the biliary tree structure. It has been proven to be useful in diagnosis prior to operation or non-surgical treatment, particularly, obstructive stones can be visualized by using a transparency technique. As experiments demonstrated, the proposed method can be used as a useful tool for the visualization of 3-D structure of biliary tree in clinical applications.