Oxidative stress (OS) may affect natural fertility and the results of assisted reproduction techniques (ARTs). Subfertility associated with polycystic ovary syndrome (PCOS) may be related to OS. This process may intensify during controlled ovarian stimulation (COS) for ARTs because of increased ovarian metabolic activity and hypoestrogenism with the use of gonadotropin-releasing hormone agonists (GnRHas). The objective of this study was to investigate the presence of systemic OS in non-stimulated cycles and to determine OS markers (malondialdehyde [MDA], advanced oxidation protein products [AOPP], hydroperoxides [FOX], glutathione [GSH], and vitamin E) during COS in non-obese infertile women with and without PCOS who were subjected to ARTs. A prospective cohort study was conducted on non-obese women (16 with PCOS, and 60 ovulatory patients with infertility due to male and/or tubal factors). The OS markers were determined during the following time-points: the follicular phase of the natural cycle (D1), after pituitary downregulation with GnRHa and before the use of gonadotropins (D2), on the day of administration of human chorionic gonadotropin (D3), and at oocyte retrieval (D4). Intergroup analysis showed that serum MDA concentrations were higher in the PCOS group at D3 (P=0.048) and D4 (P=0.002). On an intragroup analysis, the control group had higher MDA concentrations at D2 than at D1 (P=0.01) or D4 (P=0.004). The AOPP concentrations were higher at D2 (P<0.0001), D3 (P<0.001) and D4 (P<0.0001) compared to D1. The FOX concentrations were lower at D2 (P<0.0001), D3 (P<0.0001), and D4 (P<0.001) than at D1. Serum GSH concentrations were significantly higher at D4 than at D1 (P=0.02). An intragroup analysis of the PCOS subjects showed that the five OS markers did not differ significantly among the four time-points when they were analyzed (D1, D2, D3 and D4). In conclusion, non-obese infertile women with PCOS showed evidence of systemic OS after COS with gonadotropins for ICSI. On the other hand, non-obese ovulatory infertile women, and women with infertility due to male and/or tubal factors showed a possible systemic oxidative balance until the final of COS.