A database for comparing exonic architectures within sets of orthologous transcripts, offering user-friendly web interfaces and extensive visualization tools. JuncDB covers nearly 40 000 sets of orthologous transcripts spanning 88 eukaryotic species. The database can be queried and browsed, and the results are given in both textual and graphical ways. Users can query the database by providing transcript/gene/protein IDs and/or by selecting a set of species. Thus, JuncDB makes it possible to investigate the gene architecture of specific genes or compare architectures across selected species in a genome-wide fashion. By matching the comparative gene architecture data to the phylogenetic species tree, JuncDB makes it possible to infer intron gain and loss events, and therefore also to study the potential functional roles of specific introns.