Three species of resident Gyps vulture are threatened with extinction in South Asia due to the contamination of domestic ungulate carcasses with the drug diclofenac. Observed rates of population decrease are among the highest recorded for any bird species, leading to total declines in excess of 99.9% for the Oriental White-backed Vulture Gyps bengalensis in India between 1992 and 2007. Vultures have declined in Nepal, but quantitative information on the rate and scale of decreases is unavailable. Road transect surveys for vultures, following the same route, methodology and timing, were undertaken in lowland areas of Nepal for seven years from 2002 to 2011. The seven survey transects followed Nepal’s East-West highway and covered 1,010 km in three years of the survey, and 638 km in the remaining four years. Slender-billed Vultures G. tenuirostris were very scarce, with a maximum of five individuals in 2002 and none recorded in 2010 and 2011. Oriental White-backed Vultures were most commonly recorded, but decreased from 205 to 68 birds over the survey period, with an estimated annual rate of decline of 14% a year. If population decreases commenced in Nepal in the same year as in India, then White-backed Vultures in Nepal have declined by 91% since the mid-1990s. Few resident Gyps vultures remained in Eastern and Central regions of Nepal, with just one, nine and six birds recorded in the three surveys that covered these regions. The majority of threatened Gyps vultures in lowland Nepal are now found in Western and Mid Western regions, where conservation efforts have been focused in the last six years. Removing veterinary diclofenac from across the country and continuing to manage effective “vulture safe zones” are essential to conserve Nepal’s remaining vulture populations.