The aim of this paper is to develop a registration methodology in order to combine anatomical and functional information provided by thoracic/abdominal computed tomography (CT) and whole-body positron emission tomography (PET) images. The proposed procedure is based on the incorporation of prior anatomical information in an intensity-based nonrigid registration algorithm. This incorporation is achieved in an explicit way, initializing the intensity-based registration stage with the solution obtained by a nonrigid registration of corresponding anatomical structures. A segmentation algorithm based on a hierarchically ordered set of anatomy-specific rules is used to obtain anatomical structures in CT and emission PET scans. Nonrigid deformations are modeled in both registration stages by means of free-form deformations, the optimization of the control points being achieved by means of an original vector field-based approach instead of the classical gradient-based techniques, considerably reducing the computational time of the structure registration stage. We have applied the proposed methodology to 38 sets of images (33 provided by standalone machines and five by hybrid systems) and an assessment protocol has been developed to furnish a qualitative evaluation of the algorithm performance.