Background: Polycystic ovary syndrome (PCOS) as a common cause of infertility is the endocrine disorder among reproductive-aged women. Nevertheless, the management and treatment of this major problem is not deterministic, and surrounded by many controversies. Objective: In this study the effects of betanin, as red pigment present in red beetroot, in the PCOS induced rats are evaluated. Methods: Sodium valerate was injected intraperitoneally into wistar female rats to induce PCOS for 25 days. The rats were randomly divided into five groups: a normal control group without sodium valerate, Sham (sodium valerate-induced PCOS) group received 0.5 ml distilled water , metformin group and two groups that received betanin at doses of 8 and 16 mg/kg/ day for 30 days after they were administered sodium valerate. The Glucose, lipid profile, gonadotropine hormones were determined using calorimetric assays in PCOS induced rats. Histological examinations were carried out on hematoxylin-eosin stained sections using light microscopy. Results: When compared with sham, betanin caused low ovarian cysts with a high incidence of ovarian primary, antral, graafian follicles and corpus luteum. The plasma glucose, cholesterol, LDL and LH levels were found to be diminished significantly in rats with PCOS whereas plasma HDL and FSH levels were significantly increased. Conclusion: The betanin affected the cysts and follicles of the PCOS induced rats.