Alternative splicing is a widespread cellular phenomenon, which regulates gene expression in eukaryotic genomes. Availability of accumulating transcript and genomic sequence data has lead to generation of a wide-range of alternative splicing databases. Generally the available databases focus on mammalian transcriptomes. Here, we present two new alternative splicing databases for the model organisms, Drosophila melanogaster and Caenorhabditis elengans. Databases presented here allow the end-users to perform in-depth analysis of the alternative splicing events for their gene of interest. Utility of our databases are illustrated by presenting the extensively alternatively spliced DSCAM gene from Drosophila melanogaster and alternative splicing of the splicing regulatory factors U2AF, rsp-7 and swp-1 of Caenorhabditis elengans. In addition, using these two new splicing databases, we show that the majority of alternative splicing in both genomes is due to cassette exons.