Investigations of human somatosensory perception have demonstrated robust interactions between the submodalities of pain and touch, and there is increasing recognition that the systematic assessment of somatosensory perception in disorders characterized by persistent pain such as Temporomandibular Disorder (TMD) would greatly aid diagnosis and evaluation of treatment efficacy. To better understand the pathophysiological mechanisms underlying TMD, we investigated cortical processing interactions that occur between innocuous and noxious cutaneous input using functional magnetic resonance imaging (fMRI). Innocuous vibrotactile stimulation and noxious skin heating were delivered separately and concurrently to the hand of women with TMD and to pain-free, gender-matched controls (HC). Cortical responses evoked by innocuous vibrotactile stimulation alone differentiated TMDs from HCs, and the differences between the groups suggest cortical plasticity in TMD which primes areas to respond to innocuous vibrotactile input that normally would not, including parts of the pain matrix and auditory cortex. In contrast, pain ratings and cortical responses to noxious heat alone did not differ significantly between TMDs and HCs. However, additional group differences emerged in the cortical patterns characterizing interactions between somatosensory submodalities in subjects with and without TMD during concurrent stimulation that could not be explained exclusively by group differences in the response to innocuous vibrotactile stimulation. Some of these differences in the interaction of innocuous and noxious somatosensory inputs were correlated with the severity of the TMD patients’ clinical pain despite the fact that no significant correlations were observed between TMD pain and responses to vibrotactile or noxious heat stimulation alone. This suggests that cortical processing interactions between somatosensory submodalities more closely reflect individual experiences of persistent clinical pain than does the unimodal processing of innocuous vibrotactile or noxious heat input alone.