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To evaluate the reproductive and metabolic effects of L-carnitine plus metformin in clomiphene citrate (CC) resistant obese polycystic ovary syndrome (PCOS) women. A double-blinded randomized controlled clinical trial, clomiphene-citrate resistant obese women were allocated randomly to receive CC plus metformin and L-carnitine (n = 138) or CC plus metformin and placebo (n = 136). The primary outcome was clinical pregnancy rate. The secondary outcomes were hormonal and metabolic profile changes in addition to ovulation and first trimester (13 weeks) miscarriage rates. Clomiphene-citrate, L-carnitine, and metformin group showed significant improvement in the menstrual regularity, ovulation rate, and pregnancy rate compared to CC plus metformin and placebo group (29% vs. 9%, 34.7% vs.11%, and 28.2% vs. 6.6%, respectively). No statistically significant difference in the miscarriage rate between the two groups (p = .08). After three months of treatment, the reduction in body mass index (BMI) was non-significant (p = .061) between both groups. The hormonal and metabolic parameters were more significantly improved in the L-carnitine group compared with the placebo group. l-Carnitine may act synergistically with metformin for improvement of reproductive performance, insulin resistance, and lipid profile in clomiphene-resistant obese PCOS women.