Identifying the natal origins of brood parasites is a major challenge that usually requires labor-intensive searching for nests of host species. Stable isotope analysis of feathers and other body tissues of parasitic young could be a possible tool for determining natal origins if tissues reflect the isotopic composition of the diet fed to nestlings. We measured the carbon (13C) and nitrogen (15N) isotope compositions of feathers for two age-classes of brown-headed cowbirds Molothrus ater at the Konza Prairie Biological Station near Manhattan, Kansas: nestlings raised by five species of songbird hosts in two different habitats, and juveniles captured after independence. Isotope values from cowbird nestlings did not differ among host species and we were unable to assign juvenile cowbirds to their natal hosts. However, nestlings raised in grassland habitat had feathers that contained significantly higher δ13C values and lower δ15N values than nestlings raised in shrub habitats. In addition, independent juveniles had isotopic signatures that were similar to cowbird nestlings raised on shrub habitats. Although dickcissel Spiza americana comprised the majority of samples from shrub habitats, our conclusions reflect the natural pattern of parasitism at the site and should be representative of cowbirds raised at Konza. We conclude that stable isotope analysis of feathers is effective for determining the natal origins of parasitic young if isotope values from nestlings are isotopically distinct among habitats.