To assess the latent factor structure of clinical examination findings obtained from temporomandibular disorder patients, exploratory factor analysis was used to examine the relationships of a large number of variables obtained from a clinical examination to a smaller number of latent variables, or factors. Two independent samples of patients - an initial sample that consisted for 330 patients who complained of facial pain and a validation sample of 161 additional patients - were examined to determine whether the factor structure was reliable. A principal axis factor analysis with varimax rotation was used for both sets of data. The factor structure for the two samples was consistent between the two sets of data. Results identified two muscle pain factors (an intraoral muscle factor an an extraoral muscle factor), two unilateral jaw pain factors, and two factors that concern joint noise clicking (clicking and crepitus). The implications of these findings for the current nosologic systems for temporomandibular disorders are discussed.