Neandertals clearly interbred with the ancestors of non-African modern humans, but many questions remain about our closest ancient relatives. Prüfer et al. present a 30-fold-coverage genome sequence from 50,000- to 65,000-year-old samples from a Neandertal woman found in Vindija, Croatia, and compared this sequence with genomes obtained from the Altai Neandertal, the Denisovans, and ancient and modern humans (see the Perspective by Bergström and Tyler-Smith). Neandertals likely lived in small groups and had lower genetic diversity than modern humans. The findings increase the number of Neandertal variants identified within populations of modern humans, and they suggest that a larger number of phenotypic and diseaserelated variants with Neandertal ancestry remain in the modern Eurasian gene pool than previously thought.