In order to further study of the Neandertal mtDNA gene pool, we analyzed the amino acid composition and extent of amino acid racemization in 15 bones found in the Vindija Cave (Croatia). Seven samples proved to have a high content of amino acids, an amino acid composition similar to that of the contemporary bone, and a low level of racemization of aspartic acid, alanine and leucine. One of the samples was dated by AMS to over 42,000 years B.P. and used for a total of five DNA extractions. Following the earlier described approach, a total of 356bp of HVR 1 and 272bp of the HVR 2 were reconstructed from the Vindija sample. The results do not exclude that interbreeding between Neandertals and modern humans may have taken place, but they show that even if it occurred, Neandertals did not end up contributing mtDNA to the contemporary human gene pool. Despite the fact that more extensive sampling of Neandertals is obviously desirable, the current sequences indicate that: a) the diversity of Neandertals is so restricted that it is highly unlikely that a Neandertal mtDNA lineage is divergent enough to form an ancestral lineage to some modern Europeans, and b) Neandertal seem to have been similar to modern humans in having a low species-wide mtDNA diversity. In the case of humans, the low genetic diversity seen both in mtDNA and nuclear DNA sequences is likely to be the result of the rapid expansion from a population of small size. Thus, if the Neandertals had a low diversity, this may indicate that they had expanded from a small population. Analyses of further Neandertal specimens will reveal if a population history similar to that seen in modern humans underlies the reduced diversity in Neandertals.