Estimating indices of abundance of threatened species is crucial to preserving biodiversity. Over the last few decades, noninvasive genetic sampling has proven to be a more straightforward and less expensive approach than capture—mark—recapture analyses. In particular, molted feathers have become extremely popular for the monitoring of bird populations. Diagnostic molecular markers such as microsatellites, however, are still not available for many avian species of conservation concern. Highly polymorphic genes of the major histocompatibility complex (MHC), on the other hand, have become reasonably accessible during the last few years. We tested the suitability of MHC profiles as DNA fingerprints to assist the identification of individuals of a scavenger difficult to monitor through traditional approaches, the Andean Condor (Vultur gryphus). To achieve this aim, we isolated polymorphic and putatively functional genes of MHC class I (exon 3, 6 alleles) and MHC class IIB (exon 2, 11 alleles). Single-strand conformational polymorphism and direct sequencing of MHC genes, combined with molecular sexing and inference of age class from feather color, allowed us to identify 80 different individuals from 110 molted feathers collected at roost sites. Inferred sex and age ratios were concordant with previous studies relying on direct observations. Among adults, the number of males was double that of females; among juveniles, this ratio was inverted. Besides providing valuable data regarding genetic variation at functionally important genes related to resistance to pathogens, we demonstrate additional potential of polymorphic MHC loci beyond their well-known role in evolutionary ecology.