A quality control method is described for verifying that the coordinate systems of a PET and MR image from the same subject have the same relative left-right orientation. Such ambiguities can arise, for example, at the coordinating center receiving data from many institutions in large multisite studies. In this study, image registration was performed on the PET/MR image pair. The MR image was then reflected (left/right reversed) and the image registration was performed again. A comparison of the values of the cost function describing the accuracy of the registration was used to identify the correct relative orientation. In 122 studies using data with known orientations, 100% accuracy of the method was observed.