A study was designed to measure noninvasively the deep temperature of the temporomandibular joint (TMJ) region and corresponding regions of the masticatory muscles at rest. With a transcutaneous probe, the deep thermometry of the right and left anterior (Ta) and the posterior portion (Tp) of the temporal muscles, the mid-portion of the superficial belly of the masseter muscles (Mm), and the TMJ regions were measured. In 20 normal male subjects, the deep temperature of the Ta region (mean 36.342-degrees-C), the Tp region (mean 36.345-degrees-C), and the TMJ region (mean 36.06-degrees-C) was higher than that of the Mm region (mean 35.897-degrees-C) at rest. In addition, no differences in the deep temperature were observed between the right and left Ta, Tp, Mm, and TMJ regions at rest. All of the normal subjects showed differences between the right and left TMJ region of less than 0.3-degrees-C. In 10 patients with craniomandibular disorders, however, eight patients showed differences of more than 0.3-degrees-C between the asymptomatic and asymptomatic TMJ region. Because of high sensitivity and specificity, the deep thermometry measurements can provide useful non-invasive information.