Background: Some evidence indicated that the autoimmune responses are contributed in etiology of female infertility and controlled ovarian stimulation (COH) may have impact on hu-moral immunity by the time of embryo transfer and concluded that further studies are required. This study was conducted to evaluate the effect of COH with gonadotropins on the serum levels of autoantibodies in the women who underwent in vitro fertilization (IVF)/ intracytoplasmic sperm injection (ICSI) cycles and to compare basal levels of these autoantibodies be-tween groups according to history of COH.Materials and Methods: In this prospective cohort study the volunteered infertile women who underwent IVF/ICSI cycles, were recruited with regard to the inclusion criteria, from Octo-ber 2014 to March 2016 in the Royan Institute. The COH was performed according to standard long GnRH agonist protocol. The mean levels of the autoantibodies including anti-nuclear (ANA), anti-smooth muscle, anti-ovarian (AOA), anti-mito-chondrial, anti β2-glycoprotein I, anti-parietal cell (PCA) and anti-follicle-stimulating hormone (FSH) antibodies were meas-ured at three time points: on the 3–5 days of the menstrual cy-cle, one week after starting of COH and on the ovum pick-up (OPU) day. Data analysis was done using independent sample t test and one-way analysis of variance (ANOVA), followed by the Tukey post hoc test.Results: Of all participants (n = 189), 73 women had history of COH and 116 women did not have such history. The analy-sis indicated that the autoantibodies changes during COH were similar in both groups. COH has no significant impact on the level of autoantibodies one week after stimulation and on ovum pick-up day. The mean levels of autoantibodies before stimu-lation were compared among the patients groups according to different cause of infertility. The analysis revealed that patients with unexplained factor had higher mean level of PCA than those with male factor (35.8 ± 20.9 vs. 8.5 ± 2.6; P=0.02) and those with PCOS (35.8 ± 20.9 vs. 7.9 ± 4.3, P=0.05).Conclusion: No significant effect of COH was found on the studied autoantibodies by the time of OPU; however, more re-searches with specific autoantibodies profiles on this topic re-quire to be undertaken to draw appropriate conclusion.