The objective of this study was to assess changes in levels of clinical temporomandibular (TMD) pain in relation to phases of the menstrual cycle. TMD cases were 35 women not using oral contraceptives (OCs); 35 women using OCs; and 21 men. Controls were 35 normally cycling women without TMD or other chronic pains. Subjects kept daily diaries over three menstrual cycles, reporting average and worst pain, general and premenstrual symptoms. Data were subject-centered and de-trended using the residuals from a random-effects linear regression model. To test for cyclic variation, cycles were standardized to 28 days and data were grouped into 9 periods/cycle (Days 1-3, 4-6, em leader, 22-24, 25-28). Overall levels of average pain, worst pain and symptoms did not differ across TMD subject groups. For worst pain, multivariate analysis of variance revealed a statistically significant difference across 3-day periods for normally cycling women with TMD (P=0.011) and for women using OCs (P=0.017). In both groups, TMD pain levels rose toward the end of the cycle and peaked during menstruation. In women not using OCs, there was a secondary pain peak at Days 13-15, around the time of ovulation. This peak was not seen in women using OCs. There was no statistically significant difference over time periods for men (P=0.94). Similar patterns were found for average pain, as well as PMS symptoms and general somatic symptoms. These results suggest that TMD pain in women is highest at times of lowest estrogen, but rapid estrogen change may also be associated with increased pain.