To evaluate the incidence of immune abnormalities in patients with endometriosis and primary or secondary infertility.This study analyzed the incidence of alloantibodies and autoantibodies in 100 women with endometriosis and 62 patients with unexplained infertility without endometriosis who enrolled in an assisted reproduction program at the Colombian Fertility and Sterility Center from January 1, 1996, to May 30, 1997. The alloimmune status of the women was determined by testing for the presence or absence of antileukocyte antibodies. The autoimmune studies included antinuclear antibodies, antiphospholipid antibodies and lupus anticoagulant antibody.Negative titers of IgG antipaternal antibodies were identified in 34% of patients with primary infertility and in 34% of women with secondary infertility and a history of pregnancy losses. Positive titers of antinuclear antibodies were found in 27% (27/100) of the group of patients with endometriosis; of them, 30% (15/50) had primary infertility and 24% (12/50), secondary infertility. The average titer was 1/80. Forty-eight percent of the infertile patients (48/100) showed titers of antiphospholipid antibodies for IgG and IgM; 46% of these patients had primary infertility (23/50) and 50% (25/50), secondary infertility. This was significantly higher than in controls (P < .05). Two patients were positive for lupus anticoagulant antibody. In the group of patients with unexplained infertility without endometriosis, the incidence of antinuclear antibodies was 17.7% and of antiphospholipid antibodies, 30.6%.For women with endometriosis, alloimmune and autoimmune evaluation is recommended prior to their undergoing assisted reproduction in order to provide appropriate therapy for each case.