Abstract: Population genetics studies based on the analysis of mtDNA and mitochondrial disease studies have produced a huge quantity of sequence data and related information. These data, classified as RFLPs, mtDNA SNPs, pathogenic mutations, HVS1 and HVS2 sequences, and complete mtDNA sequences, are distributed in databases differently organised:: MITOMAP, HVRBASE, mtSNPs and mtDB. The two latter databases more or less report frequency data associated with the mitochondrial SNPs, while MITOMAP simply associates the mtSNP to the different phenotypes. HmtDB, stores human complete mitochondrial genomes annotated with variability data estimated through the application of specific algorithms implemented in an automatically running Variability Generation Work Flow (VGWF). Another Work Flow, called Classification Work Flow (CWF), is implemented to perform the automatic classification of newly sequenced genomes. The aims of HmtDB are to collect and integrate all human mitochondrial genomes publicly available, to produce and provide the scientific community with site-specific nucleotidic and aminoacidic variability data estimated on all available human mitochondrial genome sequences through the automatic application of VGWF, to allow researchers to analyse their own complete or partial mitochondrial genomes in order to automatically detect the nucleotidic variants respect to the revised Cambridge Reference Sequence (rCRS) and to predict their haplogroup paternity. At present, 1255 genomes classified according to their continental origin are stored in HmtDB.