Background: Soy isoflavones (SI) has estrogenic effect in tissues by binding to estrogen receptors and might be beneficial for women with Polycystic Ovarian Syndrome (PCOS) by reduction in testosterone, cholesterol , Insulin , weight gain, inflammatory markers and oxidative stress. Methods: The study was plane to examine the effect of various levels of SI on nutrient intake, digestibility, lipid profile, insulin and reproductive hormones of estradiol-valerate (4mg/rat/IM) PCOS induced rat models. Thirty-Six Wistar 45 days old rats weighing 95 ± 5g were divided into 4 groups, each having 9 rats: C (control: without SF), SF10 (SF 0.10g/Kg BW), SF15 (SF 0.15g/Kg BW) and SF20 (SF 0.20g/Kg BW). SF was given through the oral gavage. Food and water were offered ad libitum and intake was recorded daily. Body weight was recorded on weekly basis. During last week of trial, collected feces by total collection method and blood samples were used to calculate nutrient digestibility and biochemical analysis respectively. The Completely Randomized Design and LSD test were used to analyze the data. Results: The significant results were observed in female rats fed SF10, SF15 and SF20 compared to C. Estrogen, progesterone and prolactin were (P<0.05) high in rats fed SF diet that was 4 and 30% increase from C respectively. Insulin, Testosterone, FSH and LH were lowest in rats fed diet SF20. Significant (P<0.05) reduction in cholesterol was observed in rats fed SF15 and SF20 as compared to C. Serum HDL was improved (P<0.05) in all SIF 0.10 , SIF 0.15 and SIF 0.20 as 26.88±1.59 (mg/dl), 32.40±1.42 (mg/dl) and 53.44±1.50 (mg/dl) in comparison to PC. Serum LDL was significantly reduced to 68.89±4.36 (mg/dl) in SIF 0.20 , and to 108.20±4.14 (mg/dl) in SIF 0.15 whereas, insignificant reduction was observed in SIF 0.10 (127.75±4.62 mg/dl) as compared to PC. Highly significant reduction was noted in triglycerides level in SIF 0.20 as 115.00±2.04 (mg/dl), however, significant reduction was observed in both SIF 0.10 and SIF 0.15 as compared to PC after three months of treatment with soy isoflavones.Conclusions: It is concluded that soy isoflavones have potential role on reproductive hormones, insulin levels, weight, lipid profile and nutrient digestibility in PCOS induced rats.