Autoimmunity may play a role in endometriosis. The association between endometriosis and RA remains unknown. This study was conducted to identify any evidence for this relationship.This 13-year, nationwide, population-based, retrospective cohort study analysed the risk of RA in a cohort of individuals with endometriosis. We investigated the incidence of RA among patients with endometriosis using data from the Longitudinal Health Insurance Database 2000, which is maintained by the Taiwan National Health Research Institutes. We used propensity scores to match comorbidities in the two cohorts. Kaplan-Meier analysis and Cox proportional hazard model were employed to analyse the association between endometriosis and RA among patients with different potential risks.Patients with endometriosis [adjusted hazard ratio (HR) 1.75, 95% CI 1.27, 2.41], aged ≥45 years (adjusted HR 1.50, 95% CI 1.06-2.13) and with autoimmune disease (adjusted HR 6.99, 95% CI 2.84-17.21) had a significantly higher risk of RA. The analyses also showed that when stratified by age, comorbidities and medication use, the risk of RA in patients with endometriosis was also higher than in those without endometriosis.This 14-year, nationwide, population-based retrospective cohort study revealed that patients with endometriosis have a higher risk of RA. In the clinical management of patients with RA, rheumatologists should be especially mindful of the possibility of underlying endometriosis.