Androgen action on sex accessory organs influences rodent fertility but the mechanisms remain unclear and investigation is difficult without the ability to restrict androgen action in specific tissues. We employed Cre-LoxP technology to generate male mice with prostate epithelial specific androgen receptor deficiency (denoted PEARKO). In addition to prostate, these males have reduced androgen action due to tissue-selective androgen receptor (AR) inactivation in seminal vesicle, epididymis and vas deferens, while the testis is unaffected. We find that fertility of PEARKO males was severely reduced compared with littermates with prominent defects in copulatory plug formation which were smaller, softer and more friable than controls. Despite normal testis sperm production, sperm numbers were reduced in caput but increased in cauda epididymis suggesting alterations in sperm epididymal transit kinetics associated with increased rate of spontaneous acrosome reaction and abnormal flagellar morphology in PEARKO cauda epididymal sperm. While the quantitative in vitro fertilizing ability of PEARKO epididymal sperm was normal, fewer fertilized oocytes were flushed from the oviducts of females after natural mating with PEARKO males. This data show that sperm formed in mice with impaired androgen action restricted to accessory glands and epididymis are quantitatively normal in number and in vitro fertilizing function but that severe in vivo subfertility reflects other functions related to sperm transport and survival in female reproductive tract that determine fertility in vivo.