The retrieval of mitochondrial DNA (mtDNA) sequences from four Neanderthal fossils from Germany, Russia and Croatia showed that these individuals carried closely related mtDNA that is not found in modern humans. However, these results do not conclusively settle the question of the possible contribution of Neanderthals to the gene pool of modern humans, since such a contribution could have been erased by genetic drift or by the continuous influx of modern human DNA into the Neanderthal gene pool. Another problem is that if some Neanderthals carried mtDNA sequences similar to modern humans, such sequences may be erroneously considered modern contaminants when taken from fossils. Here we address these issues by analyzing 24 Neanderthal and 40 early modern human remains. The biomolecular behavior of four Neanderthals and five early modern humans was good enough to suggest DNA preservation. All four Neanderthals provided mtDNA sequences similar to those previously established in Neanderthal individuals, while none of the five early modern humans contained such mtDNA sequences. Combined with the current mtDNA data, this rules out any large genetic contribution from Neanderthals to early modern humans, but does not rule out the possibility of a smaller contribution.