Objective: To evaluate the effect of the oral melatonin supplementation on the outcomes of In Vitro Fertilization (IVF) and mitochondrial adenosine triphosphate production (MT-ATP6) gene expression in Iranian infertile couples. Study design, setting and patients: A double-blind non-randomized clinical trial was conducted, recruiting 90 infertile couples who underwent IVF between May 2015 and February 2016 at the Infertility Center of Tehran Yas Hospital in Iran. Intervention: Patients who were assigned to the intervention group received oral melatonin as a supplementation to the standard controlled ovarian stimulation (COS) with the GnRH-a long protocol. Infertile patients who were assigned to the control group only received a COS protocol. Main outcome measures: Primary outcomes were the mean number of mature oocytes retrieved and the embryo quality. Secondary outcomes were mRNA level of MT-ATP6 gene in cumulus cells, and biochemical and clinical pregnancy rate. Results: The mean number of poor quality embryos was significantly lower in the intervention group than control group (0.27 vs. 0.80; P= 0.028). The biochemical pregnancy rate and clinical pregnancy rate by fetal heart were higher in the intervention group (24% vs. 14%; P= 0.089 and 14% vs. 7%; P= 0.302, respectively), but the difference was not significant. The mRNA level of MT-ATP6 gene in cumulus cells between intervention and control groups was not statistically significant (0.931 vs.1; P˃ 0.05). Conclusion: Melatonin supplementation during COS in women undergoing IVF significantly reduce the number of poor quality embryos and it is useful in infertile couples who have poor clinical outcomes.