Background: Females of reproductive age are affected by polycystic ovary syndrome (PCOS) around the globe. Conventional methods offer symptomatic relieve, with side effects so seeds of Glycine max (L.) were used in current study. Methods: Hormonal, biochemical and histopathological improvements of Letrozole (1.0 mg/kgb.w./day) induced female Sprague Dawley rats (150-200gm) were assessed after treatment with polarity based seed extracts of G.max (L.) (10 mg/kg b.w.) By keeping cyproterone acetate (1.0 mg/kg b.w.) as positive control. Results: Statistically analyzed results (p<0.0001) showed that luteinizing hormone (LH), testosterone, aspartate aminotransferase (AST) and bilirubin decreased in PCOS rats after treatment with distilled water extract (0.5±0 mlU/ml, 0.7±0.26 ng/dl, 103±18.7 IU/L, 0.8±0.1 IU/L) as compared to positive control (1.8±0.5 mlU/ml, 20.29±0.18 ng/dl, 0134.3±43.01 IU/L, 0.9±0.0mg/dl IU/L) respectively. Increase in follicle-stimulating hormone (FSH) and estradiol level by ethyl acetate extract and progesterone level by methanolic extract were significant (1.94±0.79 mlU/ml, 978±10.5pg/dl, 15.5±8.5pg/dl) as compared to positive control (2.5±1mlU/ml, 933±3.82 pg/dl, 3.3±0.68 pg/dl) respectively, while ethyl acetate extract decreased urea, creatinine and uric acid concentration (30.3±0.5mg/dl, 0.5±0.1 mg/dl, 2.6±0.7 mg/dl) as compared to control (41.3±1.5mg/dl,0.8±0.1mg/dl,4.7±0.15mg/dl) respectively, with restoration of normal ovarian stroma from typical pearl string cystic appearance and normal hepato-renal tissues in histology. Conclusion: Active compound behind the current findings can be isolated for pharmaceutical companies in cure of PCOS.