This study was conducted to investigate the usefulness of organ-specific autoantibodies as possible markers for reproductive failure. Antithyroid and antiovarian autoantibody concentrations were measured in 78 patients with mechanical or unexplained infertility that were enrolled in an in-vitro fertilization (IVF)/embryo transfer programme with follow-up of the outcome. In all, 16 patients (20.5%) were positive for antithyroid antibodies, nine (11.5%) were positive for antiovarian autoantibodies and two (2.6%) were positive for both autoantibodies. All 23 patients who were positive for either antithyroid or antiovarian autoantibodies, or both, were defined as the study group, and 55 who were negative for autoantibodies were considered as the control group. No statistical difference in the incidence of autoantibodies was found between the patients with mechanical infertility and those with unexplained infertility. No differences were found in the mean number of oocytes retrieved, fertilization rates or mean numbers of transferred embryos between the study and the control groups. The pregnancy rate per cycle was 10.8% (7/65) in the study group, compared with 25.0% (24/96) in the control group (P < 0.05). We conclude that organ-specific autoantibodies such as antithyroid and antiovarian antibodies may serve as possible markers for reproductive failure. Further investigation is required to understand the possible immunopathological mechanism for reproduction failure in patients with organ-specific autoantibodies.