Abstract: Mitochondria are sub-cellular organelles, present in the majority of eukaryotic organisms, which play a central role in the energy metabolisms of cells. They are also involved in many other cellar processes such as apoptosis, aging and in a number of different human diseases, including Parkinson’s, diabetes mellitus and Alzheimer’s. Despite to their importance in the cell life maintenance, about the 95% of proteins, contributing to mitochondrial biogenesis and functional activities, are nuclear encoded, synthesized in the cytosol and targeted to mitochondria. The expression and assembling of these proteins are strictly dependent by the coordinated activities of the two genomes, mitochondrial and nuclear, but the molecular mechanisms and co-evolutionary processes of the cross-talk between these two genomes are still largely unknown. MitoNuc is a specialized database of nuclear encoded mitochondrial proteins in Metazoa. It provides comprehensive data on genes and proteins consolidating information from external databases. These data include: gene sequence, structure and information from ENSEMBL, protein sequence and information from SWISSPROT, transcript sequence and structure from RefSeq and UTRdb, disease information from OMIM. Each database entry consists of a nuclear gene coding for a mitochondrial protein in a given species, and reports information on: species name and taxonomic classification; gene name, functional product, sub-cellular mitochondrial localization, protein tissue specificity, Enzyme Classification (EC) code for enzyme and disease data related to protein dysfunction. For each gene and gene product the Gene Ontology (GO) classification with regard to molecular function, biological processes and cellular component is reported too. Links to external database resources are also provided. As far as the gene and transcript sequences data are concerned, in the previous MitoNuc releases they were extracted from the EMBL related entries. Due to the high level of sequences redundancy in the primary database, the majority of MitoNuc entries contained more than one transcript and coding gene sequence for the same gene, thus introducing a remarkable redundancy level that affects the effectiveness of the database for sequence analysis aims. In order to remove redundancy we generated a MitoNuc section of gene and transcript sequences derived from those organisms whose genome sequence draft has been completed and annotated in ENSEMBL. These MitoNuc entries are available in the database section called “MitoNuc Genomics” that, at present, include the following species: Homo sapiens, Rattus Norvegicus and Mus Musculus. MitoNuc can be queried using the SRS Retrieval System (http://www.ba.itb.cnr.it/srs/); the present release contains a total of 1344 entries among which 662 are collected in the MitoNuc Genomic section. The total number of species included in MitoNuc is about 64.