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 18normalF−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±0.4mm for 10‐minute scans, and 0.8°±1.2° and 2.7±1.7mm for 30‐minute scans. For MRI/MRI, the magnitude was 0.2°±0.4° and 0.3±0.2mm for 5‐minute scan intervals, and 1.1°±0.7° and 1.2±1.4mm 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.PACS numbers: 87.53.Ly, 87.57.nj, 87.57.uk, 87.57.Q‐, 87.61.jc, 87.19.xcConflict of Interest Statement: The authors do not have any conflict of interest on this research report.