Comparison of homologous sequences is an essential step for many studies related to molecular biology and evolution: to predict the function of a new gene, to identify important regions in genomic sequences, to study evolution at the molecular level or to determine the phylogeny of species. The importance of comparative sequence analysis (comparative genomics) for deciphering the genetic information embedded in the human genome is now widely recognized, and thus, projects have been set up to sequence large genomic regions of model vertebrate organisms such as mouse [1] or pufferfish [2]. Databases already contain a considerable amount of vertebrate data suitable for comparative analysis. For example, more than 1,200 homologous genes between man and rodents are available in databases [3]. Besides mammals, large sets of sequence data are also available for birds (chicken), amphibians (xenopus) and bony fishes (zebrafish, pufferfish, salmonidae), thus covering a wide range of evolutionary distances, from 80 to 450 million years of divergence. Thanks to this large and rapidly increasing amount of homologous sequences, comparative sequence analysis should be very efficient for improving our knowledge of the structure, function and evolution of vertebrate genomes. However, the search for homologous genes and interpretation of homology relationships are complex tasks that require to simultaneously handle multiple alignments, phylogenetic trees, taxonomic data and sequence-related information. Genomic sequence databases such as GenBank [4] or EMBL [5] do not include information relative to homology relationships between genes, and hence these analyses have to be done manually, which is very tedious and error prone. To respond to these problems, we have developed a database of homologous vertebrate genes named HOVERGEN [6]. This database integrates protein multiple alignments, phylogenetic trees, taxonomic data, nucleic and protein sequences, and GenBank sequence annotations. With its graphical interface, HOVERGEN allows one to rapidly and easily select sets of homologous genes and evaluate homology relationships between sequences. This chapter describes the content of this database, the procedure we use to maintain it, a few examples of application and the future developments that we plan.