The high frequency (around 0.70 worlwide) and the relatively young age (between 14,000 and 62,000 years) of a derived group of haplotypes, haplogroup D, at the microcephalin (mcph1) locus led to the proposal that haplogroup D originated in a human lineage that separated from modern humans >1 million years ago, evolved under strong positive selection, and passed into the human gene pool by an episode of admixture circa 37,000 years ago. The geographic distribution of haplogroup D, with marked differences between Africa and Eurasia, suggested that the archaic human form admixing with anatomically modern humans might have been Neanderthal. Here we show that a well-preserved Neanderthal individual from Monti Lessini, Italy, dated at approximately 50,000 years BP, was homozygous for the ancestral, non-D, allele. The high yield of exclusively Neanderthal mtDNA sequences of the studied specimen, and an accurate control of the mcph1 alleles in all personnel that manipulated the sample, make it extremely unlikely that this result might reflect modern DNA contamination. The mcph1 genotype of the Monti Lessini Neanderthal does not prove that there was no interbreeding between anatomically archaic and modern humans in Europe, but certainly shows that speculations on a possible Neandertalian origin of what is now the most common mcph1 haplogroup are not supported by empirical evidence from ancient DNA.