We present ParaDB (http://abi.marseille.inserm.fr/paradb/), a new database for large-scale paralogy studies in vertebrate genomes. We intended to collect all information (sequence, mapping and phylogenetic data) needed to map and detect new paralogous regions, previously defined as Paralogons. The AceDB database software was used to generate graphical objects and to organize data. General data were automatically collated from public sources (Ensembl, GadFly and RefSeq). ParaDB provides access to data derived from whole genome sequences (Homo sapiens, Mus musculus and Drosophila melanogaster): cDNA and protein sequences, positional information, bibliographical links. In addition, we provide BLAST results for each protein sequence, InParanoid orthologs and 'In-Paralogs' data, previously established paralogy data, and, to compare vertebrates and Drosophila, orthology data.