The purpose was to evaluate and correct the co-registration of diagnostic PET/CT and MRI/MRI images for stereotactic radiosurgery (SRS) using 3D volumetric image registration (3DVIR). The 3DVIR utilizes the homogeneity of color distribution over a volumetric anatomical landmark as the registration criterion with submillimeter accuracy. Fifty-three PET/CT and MRI (T1, T2 and FLAIR) image sets of patients with brain lesions were acquired sequentially from a hybrid PET/CT or an MRI scanner with common diagnostic head holding devices. Twenty-five sets of head 18F-FDG-PET/CT images were scanned over a 10-minute interval and 14 whole-body sets were scanned over a 30-minute interval. Fourteen sets of MRI images were acquired, and each 3-modal image set (T1, T2 and FLAIR) was scanned in sequence at time 0, ~5 and ~20 minutes. The misalignments in these "co-registered" images were evaluated and corrected using the 3DVIR. Using the head immobilization devices commonly found in diagnostic PET/CT and MRI/MRI imaging, 80%-100% of these "co-registered" images were identified as misaligned. For PET/CT, the magnitude of misalignment was 0.4° ± 0.5° and 0.7 ± 0.4 mm for 10-minute scans, and 0.8° ± 1.2° and 2.7 ± 1.7 mm for 30-minute scans. For MRI/MRI, the magnitude was 0.2° ± 0.4° and 0.3 ± 0.2 mm for 5-minute scan intervals, and 1.1° ± 0.7° and 1.2 ± 1.4 mm for 20-minute intervals. Small, but significant, misalignment is present in the co-registered diagnostic PET/CT and MRI/MRI images and can be corrected in SRS treatment planning using the volumetric image registration for improved target localization within the clinical error tolerance.