No genetic continuity between local hunter-gatherers and the first farmers in Central Europe. After the domestication of animals and crops in the Middle East some 11,000 years ago, agriculture reached most of Central Europe 7,500 BCE. The extent to which these early European farmers were immigrants or descendants of resident hunter-gatherers who adopted agriculture has been widely debated. We compared new mitochondrial DNA (mtDNA) sequences from the skeletons of late European hunter-gatherers with those from early farmers and modern Europeans. We discovered large genetic differences between all three groups that cannot be explained by population continuity alone. Most (82%) of the ancient hunter-gatherers have the same types of mtDNA, which are relatively rare in today's central Europeans. Together, these analyses provide convincing evidence that the first farmers were not descendants of local hunter-gatherers, but arrived in Central Europe at the beginning of the Neolithic.