An algorithm for reconstructing magnetic resonance cholangiography (MRC) biliary structure is proposed. The processing of MRC data can be divided into four phases. In the first phase, the region of interest (ROI) containing the liver and biliary ducts is extracted from the original volume data based on human anatomy and B-spline curve. The second phase involves segmenting the biliary ducts from the region identified in the previous phase. Because the image of biliary portion is brighter than the liver, the segmentation is started by choosing the brightest pixel in the ROI as the seed for 3D region growing. This procedure could be executed many times, depending on the provided stopping condition. In the third phase, the segmented biliary duct regions are traced to construct the biliary tree. An automated 3D tracking algorithm is proposed for this phase. This 3D tracking algorithm estimates the coordinates of the points along the medial axis of each biliary duct branch. The cross sections associated with the points along the medial axis are also calculated approximately during the tracking process. The biliary tree data structure is constructed in this phase. The biliary tree is reconstructed and rendered in the last phase. Although the proposed algorithm takes a longer time compared with the conventional approach, the reconstructed biliary tree 3D structure can provide more clearly image. A concise representation for the biliary tree can be achieved with the proposed method and provide both quantitative and structural information for clinical reference.