Aim: This study aimed to evaluate serum selenium levels and glutathione peroxidases (GPxs) activity in women with idiopathic primary ovarian insufficiency (iPOI) and in healthy fertile women. Materials and methods: This case-control study was conducted in Al-Zahra Hospital affiliated to Tabriz University of Medical Sciences, Tabriz, Iran. The iPOI group consisted of 32 infertile women with iPOI (with amenorrhea/oligomenorrhea at least for the last 4 months and FSH>40 mIU/ml) . The control group consisted of 31 age-and BMI- matched healthy fertile women. In the all participants, serum selenium levels were measured by an atomic absorption spectrophotometer, and plasma GPx activity was measured by a Glutathione Peroxidase Activity Assay Kit after about 12 hours of fasting. Results: There was a significant lower serum selenium levels in the iPOI group compared to the control group (Adjusted Mean Difference (AMD) =-15.1 µg/ml, 95% CI: -24.8 to -5.3). The plasma GPx activity was lower in the iPOI group compared to the control group, although not significantly (AMD =-67.0 U/ml, 95%CI: -194.5 to 60.3). Both groups had similar selenium dietary intake and in accordance with the recommended dietary allowance (RDA) of 55 µg/day. Conclusion: This study showed a significant decline in the serum selenium levels of women with iPOI. To determine their selenium-dependent antioxidant defence capability, as measured by GPx activity, more large-scale studies are required.