Neandertal (Homo neanderthalensis) was developed from the species Homo antecessor, which is also the common ancestor of anatomically modern humans (Homo sapiens sapiens). The analysis of Neandertal genome from three bone samples aged 38 000 years, from the area Vindija Cave, gave a sequence of more than 3 billion nucleotides which was compared with a genome of 5 people from different parts of the world. The results suggest that Europeans and Asians share 1-4% of the genome with Neandertals while Africans do not share, this supports the thesis that there was interbreeding between early anatomically modern humans and Neandertals after modern humans left Africa, but before they spread into Asia and Europe. It is also observed that modern human share 99,84% genome with Neandertal genome, but there are genes that are fixed in the modern human by positive selection after separation from Neandertals. In the sequence there was found 212 regions with changes including regions with genes involved in human cognitive development, skull morphology, metabolism, morphology and physiology of the skin, and the genes that encode for regulatory proteins. To make the analysis of ancient DNA successful it is necessary to reduce the contamination of the samples, introducing "clean room" conditions. It is also necessary to use the method of high-throughput DNA sequencing and metagenomic analysis of complex DNA mixtures that enable the recovery of isolated genomic sequences, since the ancient DNA degrades over the years. And in order to recover information about specific regions of interest, which cannot be used due to contamination, the DNA microarray approach is used.