BACKGROUND Women with endometriosis may have higher rates of autoimmune disorders, including hypothyroidism. The objective of this study was to compare the prevalence of thyroid dysfunction and autoimmune thyroid disease (AITD) between women with endometriosis and a control group. METHODS This was a cross-sectional study carried out in 148 women with surgically confirmed endometriosis and 158 controls. The mean age of the study group was 34.6 (7.1 SD) years (range 21–42) and 32.1 (7.7 SD) years (range 18–44) for controls. Serum levels of thyroid-stimulating hormone, free thyroxine and the anti-thyroperoxidase and anti-thyroglobulin antibodies were evaluated. RESULTS Thyroid disorders were identified in 20.9% of the endometriosis group and 26.5% of the control group (P = 0.25). The overall frequency of thyroid dysfunction was 12.2% and 10.8% for the endometriosis and control groups, and the frequency of positive thyroid antibodies, 14.9% and 22.2%, respectively (P = 0.20). Endometriosis stage and infertility history were not associated with thyroid dysfunction and AITD in the study group. CONCLUSIONS The prevalence of thyroid dysfunction and AITD was similar in the two study groups. Screening for thyroid disturbances in women with endometriosis is not indicated