Radiotherapy treatment planning integrating positron emission tomography (PET) and computerized tomography (CT) is rapidly gaining acceptance in the clinical setting. Although hybrid systems are available, often the planning CT is acquired on a dedicated system separate from the PET scanner. A limiting factor to using PET data becomes the accuracy of the CT/PET registration. In this work, we use phantom and patient validation to demonstrate a general method for assessing the accuracy of CT/PET image registration and apply it to two multi-modality image registration programs. An IAEA (International Atomic Energy Association) brain phantom and an anthropomorphic head phantom were used. Internal volumes and externally mounted fiducial markers were filled with CT contrast and 18F-fluorodeoxyglucose (FDG). CT, PET emission, and PET transmission images were acquired and registered using two different image registration algorithms. CT/PET Fusion (GE Medical Systems, Milwaukee, WI) is commercially available and uses a semi-automated initial step followed by manual adjustment. Automatic Mutual Information-based Registration (AMIR), developed at our institution, is fully automated and exhibits no variation between repeated registrations. Registration was performed using distinct phantom structures; assessment of accuracy was determined from registration of the calculated centroids of a set of fiducial markers. By comparing structure-based registration with fiducial-based registration, target registration error (TRE) was computed at each point in a three-dimensional (3D) grid that spans the image volume. Identical methods were also applied to patient data to assess CT/PET registration accuracy. Accuracy was calculated as the mean with standard deviation of the TRE for every point in the 3D grid. Overall TRE values for the IAEA brain phantom are: CT/PET Fusion = 1.71 +/- 0.62 mm, AMIR = 1.13 +/- 0.53 mm; overall TRE values for the anthropomorphic head phantom are: CT/PET Fusion = 1.66 +/- 0.53 mm, AMIR = 1.15 +/- 0.48 mm. Precision (repeatability by a single user) measured for CT/PET Fusion: IAEA phantom = 1.59 +/- 0.67 mm and anthropomorphic head phantom = 1.63 +/- 0.52 mm. (AMIR has exact precision and so no measurements are necessary.) One sample patient demonstrated the following accuracy results: CT/PET Fusion = 3.89 +/- 1.61 mm, AMIR = 2.86 +/- 0.60 mm. Semi-automatic and automatic image registration methods may be used to facilitate incorporation of PET data into radiotherapy treatment planning in relatively rigid anatomic sites, such as head and neck. The overall accuracies in phantom and patient images are < 2 mm and < 4 mm, respectively, using either registration algorithm. Registration accuracy may decrease, however, as distance from the initial registration points (CT/PET fusion) or center of the image (AMIR) increases. Additional information provided by PET may improve dose coverage to active tumor subregions and hence tumor control. This study shows that the accuracy obtained by image registration with these two methods is well suited for image-guided radiotherapy.