Polycystic ovary syndrome (PCOS) is the most common hyperandrogenic disorder in women and one of the leading causes of anovulatory infertility. Depletion of vital hormones in the organism, such as in the case of PCOS, has been identified as one factor contributing to poor pregnancy outcomes and associated issues in women. Vitamin D level in PCOS patients regulates fertility through membrane-bound receptors in oocytes, regulating luteinizing hormone (LH), and progesterone surges.The objective. To examine the correlation between melatonin and vitamin D3 deficiency in Iraqi pregnant women with PCOS under the age of 40.Material and methods. Two hundred women were recruited for the study and divided into two groups: patients with PCOS (n=100) and healthy females without PCOS (n=100). All participants were administered medical questionnaires, and their body mass index (BMI) was determined. Blood samples from participants were obtained for biochemical analysis to assess follicle-stimulating hormone (FSH), luteinizing hormone (LH), anti-Müllerian hormone (AMH), melatonin, and vitamin D levels.Results. The results revealed that 65% of PCOS patients were between 20 and 30 years old and healthy control persons did not show any variations based on age. Patients with PCOS had significantly (p<0.001) higher levels of LH and FSH (1.98±0.07 nmol/mL and 11.15±0.25 mIU/L, respectively) compared with healthy controls (1.06±0.02 nmol/mL and 6.67±0.25 mIU/L, respectively). The PCOS group had significantly (p≤0.01) reduced mean vitamin D3 level related to the control group. There was no significant correlation between vitamin D3 and melatonin levels in the PCOS group. The study showed that BMI was significantly higher in women with PCOS compared to healthy women. The study also found a positive relationship between BMI and AMH concentration, as well as between FSH and vitamin D3 levels in women with PCOS. However, there was no association between vitamin D3 and melatonin or BMI. Conclusion: The study found that D3 deficiency is a significant component in female PCOS patients that might be a new biomarker for PCOS in Iraqi women.