For quantification of drug's delivery using small animals measuring biochemical changes in abdominal organs based on functional images is essential. However, in those images, the object boundaries are not clearly enough to locate its shape and position. And even though the structural information is compensated using image registration technique, delineation of organs is difficult and time-consuming. So we suggested an automatic procedure for delineation of organs in mouse PET image with the aid of atlas as a priori anatomical information. Prior information was given by voxel label number. CT used to construct an atlas is transformed to match mouse CT to be segmented. For each label corresponding voxels represent the same organ. Then, mouse CT-PET pairs should be aligned to identify organ area in PET. After all images are aligned and fused each other both structural and functional information can be observed simultaneously for several organs.