Background: In Polycystic ovary syndrome (PCOS) life style and dietary changes are recommended as the first line of management; however, the optimal nutritional management is not certain yet. Polyunsaturated fatty acids (PUFAs), particularly long-chain (omega-3) PUFAs, is known to improve overall human health and its widely used in managing infertility, but its role in PCOS management is still uncertain. Objective: The purpose of this study was to assess if omega-3 fatty acids supplementation for Polycystic ovary syndrome patients will have a positive effect on body weight, Hirsutism score, Menstrual cyclicity, hormonal status and Doppler flow to the Uterine and Ovarian stromal arteries. Study Design: A randomized prospective trial. Patients and Methods: A total of 67 patients with Polycystic ovary syndrome were randomized into two groups. Group I patients who received omega-3 fatty acid 1 gram daily capsules and group II patients who received no treatment for 3 months. Changes in weight, BMI, menstrual cycle length, modified Ferriman Gallway score, serum FSH, LH ,free Testosterone levels and Doppler of ovarian stromal and uterine arteries between baseline and the 3 months study period were compared between the 2 groups. Results: After 3 months supplementation with omega-3 fatty acid capsules, there was a statistically significant decrease in menstrual cycle length in the study group in comparison to the control group. Also, there was a statistically significant decrease in the pulsatility index (PI) of the uterine artery Doppler in the study group, but there was no change in the weight, BMI, ovarian stromal blood flow. Also, measures of FSH, LH and free testosterone did not show statistically significant changes for either group. Conclusion: Omega-3 fatty acids supplementation is effective in improving menstrual cyclicity and uterine artery blood flow in patients with PCOS and may be an helpful option for some patients with PCOS especially those who have defective endometrial receptivity and subsequent infertility or repeated miscarriages because of increased uterine artery resistance.