In this paper, a normalized abdominal coordinate system is defined for abdominal atlas mapping in CT and MR volume images. This coordinate system is independent of both the abdomen size and the respiratory motion. A real-time atlas mapping algorithm based on this coordinate system is also proposed. The purpose of this algorithm is to provide initial positions for abdominal organ segmentation. This algorithm reckons in the respiration phase and the fat amount to compensate organ translations. With this algorithm, rough positions of the target organs are found rapidly, and accurate segmentation results are obtained based on the mapping results.