The August 8, 2008 issue of Cell includes a paper documenting the sequencing of mitochondrial DNA extracted from a 38,000 year old Neandertal bone (emphasis added):
A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from ?0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small.
That highlighted portion means that the mitochondrial DNA of Neandertal differed so substantially from that of humans that interbreeding almost certainly occurred rare if at all.
The researchers behind this paper are working on sequencing of the full Neandertal genome.