AbstractEpidemiological study shows inconsistent results in the association between endometriosis and Systemic lupus erythematosus (SLE). We conducted a nationwide retrospective cohort study and analyzed data from the Taiwan Longitudinal Health Insurance Research Database 2000 (n = 958,349) over a 13-year follow-up period (2000–2013). After matching 1930 SLE women with 7720 non-SLE women in a 1:4 ratio by age, we used Cox proportional hazard regression to calculate the adjusted hazard ratio (aHR) for endometriosis diagnosed after SLE. We also used a diagnosis of endometriosis with previous gynecologic surgery codes as secondary outcomes and performed sensitivity analyses using a landmark analysis. After adjustment for age, urbanization, income, length of hospital stay, and comorbidities in the age-matched group, women with SLE had a higher risk of endometriosis than women without SLE (aHR 1.32, 95% CI 1.02–1.70). When we defined endometriosis as patients with an ICD-9 endometriosis code after undergoing gynecologic surgery, the increased risk of endometriosis in patients with SLE was not significant. Our findings suggest that the risk of endometriosis was significantly elevated in the cohort of women with SLE compared with the age-matched general cohort of women. The burden of endometriosis in SLE patients requires special attention.