Characterization of the estrous cycle and the ability to detect pregnancy are essential for the development of efficient captive breeding programs in wild mammalian species and for their conservation. We assess here the feasibility of using fecal progesterone analysis as a non-invasive method of monitoring the ovarian function of the Shiba goat as an experimental model for ruminant species. Feces and blood samples were collected sequentially from 4 female goats throughout the estrous cycle and gestation period and from 2 ovariectomized goats which were subcutaneously implanted with progesterone. The recovery rate with ether extraction was about 70% for fecal progesterone. Fecal progesterone concentrations changed dramatically in accordance with plasma progesterone during the estrous cycle and the pregnancy. Moreover, implantation and removal of progesterone capsules resulted in matched elevation and decline in fecal and plasma progesterone. The present data suggest that measurement of progesterone in feces is a potential noninvasive method of assessing the reproductive status of ruminant species.