The Himalayan musk deer (Moschus chrysogaster), an endangered species, is facing threat of extinction globally due to severe hunting for its musk, and efforts are under way in India to breed them in captivity. However, no information is available on the reproductive cycles of the species. In this study, we aimed to standardize an enzyme immunoassay (EIA) procedure for monitoring pregnancy using fecal samples. We collected fecal samples for 12 months from five captive females maintained at the Musk Deer Research Centre, Bageshwar, Uttarakhand, India. Three of these females were observed mating and gave birth, whereas two were seen mating but did not give birth. The gestation periods for the three females were 183, 185, and 199 days, respectively. High-pressure liquid chromatography revealed the presence of immunoreactive pregnanediol-3-glucuronide (PdG), progesterone, and 5α-pregnan-3α-ol-20-one (5-alpha-pregnane) metabolites in the fecal samples. We used EIAs against progesterone, PdG, and 5-alpha-pregnane to monitor pregnancy. We found PdG EIA to be a highly accurate and sensitive assay compared with the other two assays in detecting pregnancy. We conclude that PdG EIA can be used to diagnose and monitor pregnancy in Himalayan musk deer using fecal steroid analysis, at an early stage of 3 months after mating. This study would help in conservation breeding of musk deer in captivity and in monitoring the reproductive status of the species in the wild.