The Slender-billed Vulture is probably the most endangered of the three resident Gyps vulture species of the Indian subcontinent, with a population of less than 1,000 individuals in the wild. A Conservation Breeding Programme was initiated by the Bombay Natural History Society (BNHS) to save this species from possible extinction. Sex identification of individuals is important to maintain the right sex ratio to maximize breeding success in the Conservation Breeding Programme. The Slender-billed Vulture is not sexually dimorphic, hence the applicability of polymerase chain reaction based (molecular sexing) methods for sex identification was assessed, and the first ever successful application of W-specific PCR combined with ZW-common PCR for sex identification in Slender-billed Vulture (n=12) was established. The PCR method was validated by comparing results with sex identification based on the study of breeding biology of nesting pairs. The reported molecular sexing method could prove a useful tool in management of Conservation Breeding Programmes, and also in determining the sex of dead birds collected from the wild during ecological studies.