The ethanol extract of the Crotalaria juncea seeds, which showed promising antispermatogenicand antiandrogenic activities in albino mice, was taken up further for the isolation of the activefractions present in it. Two fractions that were obtained from thin layer chromatography weresubjected for testing to know their antispermatogenic and antiandrogenic activities. Afterpreliminary trials the fraction I showed maximum antifertility activity at the dose level of 200 mg/kgbody weight when administered orally to the rats for 50 days. The fraction I was found to affectspermatogenesis as well as the endocrine functions of the testis as indicated by gravimetric,histopathological and biochemical changes. Further this fraction has caused degenerative changesin the seminiferous tubules and Leydig cells of the testis. The accessory reproductive organs likeepididymis, seminal vesicles, vas deferens, prostrate, Cowper’s gland and Levator Ani muscleshowed significant malfunction. Cauda epididymal sperm count and sperm motility werereduced significantly. The treatment has also resulted in increase in the cholesterol level andalkaline phosphatase activity, and decrease in protein, glycogen, sialic acid contents and acidphosphatase activity in testis. It is noteworthy that RIA studies have shown significant reductionin serum FSH, LH and testosterone. Scanning electron microscopic observations revealedabnormalities in sperm structure.