From a public health perspective, the need for contraception has never been greater. Although the existing male-specific methods are safe and effective, increasing male options for fertility control could improve family planning. For new male contraceptive methods to have an impact, they must be acceptable to both men and women, as well as effective. It is necessary to use biologically active botanical substances or fertility-regulating agents of plant origin which are ecofriendly. There is no documented evidence referring to the male antifertility of  Azadirchta Indica (neem) botanical seed’s extract. The epididymis and vas deferens are the  sites which can be exploited for male contraception without undue side effects, it was therefore of interest to investigate the effect of alcoholic extract of old and tender AI (neem) seed as an efficient and competent male contraceptive on mouse epididymis. In this experimental case control study sixty adult healthy mice divided into two groups of 40 as the control and 20 treated ones. The treated group was administered by Iranian Botanical Azadirachta Indica seed alcoholic extract, cultivated at Dashteh Moghan (Ardabil province). The seeds of shade-dried matured drupes of A. indica were powdered and the fraction was extracted with ethanol then administered first 50 mg/kg body weight /day then 100 mg/kg body weight/day orally for 15 days, following WHO guide lines (MB-50) that specified the oral route would be the most feasible rout and standard mode of administration of a plant extract. The target organs, epididymis and vas deferens histology and histocytometric of the two groups were compared. The 50 mg /kg body weight/day showed no significant change in epididymal sperm motility.as compare to the  control. Therefore the dose was changed to 100 mg/kg B.W./day for 15 days. Histoarchitecure of epididymis and vas deferens of treated mice were affected after treatment involving disorganization of epididymal and vas deferens epithelium, pycnosis of cell nuclei and clumping of sperm. The mechanism of action of seed extract was probably via altering the hormone levels and causing androgen deprived effect to target organ. This alters vas deferens and epididymal milieu and affects the spermatozoa. It is evident that extract has potential as an antifertility agent.