Positron emission tomography (PET) provides important information on tumor biology, but lacks detailed anatomical information. Our aim in the present study was to develop and validate an automatic registration method for matching PET and CT scans of the head and neck. Three difficulties in achieving this goal are (1) nonrigid motions of the neck can hamper the use of automatic ridged body transformations; (2) emission scans contain too little anatomical information to apply standard image fusion methods; and (3) no objective way exists to quantify the quality of the match results. These problems are solved as follows: accurate and reproducible positioning of the patient was achieved by using a radiotherapy treatment mask. The proposed method makes use of the transmission rather than the emission scan. To obtain sufficient (anatomical) information for matching, two bed positions for the transmission scan were included in the protocol. A mutual information-based algorithm was used as a registration technique. PET and CT data were obtained in seven patients. Each patient had two CT scans and one PET scan. The datasets were used to estimate the consistency by matching PET to CT1, CT1, to CT2, and CT2 to PET using the full circle consistency test. It was found that using our method, consistency could be obtained of 4 mm and 1.3° on average. The PET voxels used for registration were 5.15 mm, so the errors compared quite favorably with the voxel size. Cropping the images (removing the scanner bed from images) did not improve the consistency of the algorithm. The transmission scan, however, could potentially be reduced to a single position using this approach. In conclusion, the represented algorithm and validation technique has several features that are attractive from both theoretical and practical point of view, it is a user-independent, automatic validation technique for matching CT and PET scans of the head and neck, which gives the opportunity to compare different image enhancements.