<p>Background: Polycystic ovary syndrome (PCOS) is a multifactorial, metabolic disorder. Characteristics are chronic anovulation, polycystic ovaries and hyperandrogenism. The aim of this study was to determine the effect of omega-3 supplementation on visfatin, adiponectin, and anthropometric indices in PCOS women.<br /> Methods: The study was a randomized double blind placebo-controlled clinical trial. It was conducted on 84 women with polycystic ovary syndrome (26.92&plusmn;5.05 years, BMI=31.69 <em>Kg/m²</em>) who referred to the fertility and infertility research center and Shahid Sadoughi hospital in Yazd. After the examination, evaluation and paramedical assessment by obstetrician, they were recruited. They took 3 capsules of omega-3 (each one contained 180 <em>mg</em> EPA and 120 <em>mg</em> DHA) or placebo (each contained 1 <em>g</em> paraffin) daily for 8 weeks. Statistical analysis was paired T-test and student T-test, and a p&lt;0.05 was considered statistically significant.<br /> Results: After the intervention, visfatin concentration did not change in neither groups. But, at the end of the study, the mean of adiponectin concentration increased (p&lt;0.001) in omega-3 group. Moreover, the mean of changes in this factor was significantly different between groups (p&lt;0.005). FSH did not change in two groups of the study. However, the mean of LH decreased about 1.74 <em>mlU/ml</em> in omega-3 group (p&lt;0.005). The mean of change of LH/FSH ratio between groups was significant (p&lt;0.05). After the intervention, prolactin did not meaningfully change in both groups.<br /> Conclusion: Our results showed that 8 weeks of supplementation of omega-3 may have some beneficial effects on PCOS biochemical characteristics such as LH, LH/FSH, and adiponectin.</p>