Polycystic ovary syndrome (PCOS (is a complex disorder which reflects variable clinical symptoms. There is considerable heterogeneity of symptoms and signs among women with PCOS, and for an individual, these may change over time. The genetic base of PCOS is not clear and no concrete genetic correlation was built with PCOS. The current study showed the presence of multiple peripheral small cysts 5-9 mm also there was an increase in ovarian volume 3.7-3.9 cm and change in ovarian dimensions with the ovary being more spherical. 20.8% of the PCOS patients included in this study found to have hyperthyroidism. Thethyroid stimulating hormone-TSH level was significantly higher 17.34±5.12μIU/ml in 4 POCS patients with thyroid hormones disturbance than the level in POCS patients without thyroid disturbance or healthy control group )2.19 ±0.47 and 2.33±0.44 μIU/ml respectively(. On the other hand, the rest of POCS patients with thyroid hormones disturbance 7 Patients showed lower significance levels of triiodothyronine-T3 and thyroxine-T4 (0.96±0.029 and 51.33± 10.96 n.mol/L respectively) than other groups. At the molecular analysis five substitution thyroid peroxidase genes -TPO mutations were detected in 5 patients with PCOS and thyroid hormones disturbances. Three of them were detected in exon 8 and two in exon 9. The missense substation mutations detected in this study involve one transition of T to C (c.904T>C) and 4 transversion of C to G, C to A and G to C (c.904T>C, c.1280C>G, c.1265C>A, c.1617G>C and c.1603G>C respectively).