Inhomogeneous magnetization transfer (ihMT) and magnetization transfer (MT) have differential sensitivity to myelin and can be used to characterize cortical gray matter. We compared cortical surface-based analyses of ihMT and MT between multiple sclerosis (MS) patients and age-matched healthy volunteers. IhMT at mid-thickness decreased less than MT in most cortical regions of MS patients. Integrated signal across cortical depth showed less spatial variability and clear decrease of ihMT but less than MT. As ihMT is understood to be more specific to myelin than MT, these findings suggest loss of cortical nonmyelinated cells and structures exceed cortical myelin loss in MS.