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Polycystic ovary syndrome (PCOS) is characterized by reproductive disorder and increased risk of metabolic syndrome. This study aimed to assess the metabolic parameters in the cord blood of neonate of mothers with obese PCOS and comparison with non-obese PCOS and controls. This retrospective cohort study was conducted in Arash and Kamali Hospital in 2017-2018. The biochemical test was conducted on 78 neonates from obese PCOS mothers, 78 neonates from non-obese PCOS mothers, and 78 neonates from healthy mothers. Finally, cord blood lipid