Endometriosis is associated with a number of immunologic alterations. It has been suggested that autoimmune disorders could be more frequent in patients with endometriosis. The aim of this study is to ascertain whether the prevalence of two well-known autoimmune diseases [systemic lupus erythematosus (SLE) and Sjögren's syndrome (SS)] is increased in women with endometriosis. The clinical charts of four different populations assisted at the same hospital were manually revised: (i) SLE population (n = 120), (ii) SS (n = 22), (iii) endometriosis (n = 342) and (iv) control population (n = 501 consecutive unselected asymptomatic women). Among SLE women, the prevalence of endometriosis was 1.67% (2/120), similar to the 4.39% prevalence of the control group (22/501), the OR being 0.37 [95%CI 0.09-1.59]. Among SS women, the prevalence of endometriosis was 9.09 (2/22), also similar to the control group OR 2.17 [95%CI 0.48-9.90]. In the same way, when comparing endometriosis cases with asymptomatic women, similar frequencies of SLE (0.58% and 0.2%) and SS were found (0% and 0%). Women with endometriosis do not have an increased prevalence of SLE or SS.