Mitochondria are a 'cell within a cell'. Their, relative to the complete cell, limited number of proteins, offer the opportunity to obtain, in the coming decade, an understanding of the processes that occur within them. Furthermore their evolutionary origin from a bacterium, the rapid accumulation of mitochondrial genomics data, and their relevance to human disease make them a very interesting subject for comparative analyses using bioinformatics techniques. We specifically focus on the prediction of the function of mitochondrial proteins and on the pathways that connect them. In the past we have e.g. correctly predicted a new protein involved in the oxidative phosphorylation Complex I and the involvement of the protein frataxin in the mitochondrial assembly of FeS clusters. Our current interests are into proteins involved in the response and defense against oxidative stress, in mitochondrial transport, in mitochondrial DNA maintenance and in the fission and fusion of mitochondria.