Previous research suggests that a co-morbid relationship exists between migraine and endometriosis; however, results have been inconsistent. In addition, female hormones, which are important in the pathogenesis and management of endometriosis, have been reported to precipitate migraine attacks and may confound the results. The aim of this population-based cohort study was to explore the relationship between migraine and endometriosis in women of reproductive age (18-51 years). Data were derived from the National Health Insurance Research Database of Taiwan, which contains outpatient and inpatient records from 2000 to 2007. Our study cohort included 20,220 endometriosis patients and 263,767 controls without endometriosis. We analyzed the prevalence of migraine in these women as recorded during the eight years of the database. Our results found that patients with endometriosis were more likely to suffer migraine headaches compared to controls (odds ratio [OR], 1.70; 95% confidence interval [CI] [1.59, 1.82]; p<0.001). In addition, the co-morbid association between migraine and endometriosis remained significant after the data were controlled for age and frequently utilized hormone therapies (OR, 1.37; 95% CI, [1.27, 1.47]; p<0.001). The results of this cohort study support the existence of a co-morbid relationship between migraine and endometriosis, even after adjusting for the possible effects of female hormone therapies on migraine attacks.