Recent studies have investigated the role of autoimmune factors in implantation in women undergoing fertility treatment. The most commonly studied antibodies include antiphospholipid antibodies (APA), antithyroid antibodies (ATA), antinuclear antibodies (ANA), antigliadin antibodies, antiovarian antibodies (AOA), and antisperm antibodies (ASA). Several published reports indicate that positive APA are found more frequently in patients undergoing in vitro fertilization (IVF) or who have failed IVF. Although the prevalence of APA is higher among women undergoing IVF, their presence does not appear to influence the outcome of pregnancy, miscarriage, or live birth rate. Thrombophilias have been thought to cause a state of hypercoagulation at the implantation site impeding the connection between maternal and fetal blood flow, ultimately resulting in miscarriage. Screening for thrombophilias in women who are infertile or in those with implantation failure remains controversial and should not routinely be performed in women undergoing IVF.