Recent advances in homologue recombination based bacterial artificial chromosome (BAC) engineering have greatly simplified knock-in, knock-out and random integration based transgenic mice technologies. Despite the rapid advances in ldquowetrdquo BAC engineering, efficient bioinformatics tools for choosing the appropriate BACs and designing the targeting construct with gene specific homology arms has not been described. Here we introduce a novel bioinformatics tool called eBAC (electronic BAC) that designs, in a high throughput way, all the necessary constructs for BAC engineering. The input to eBAC is a list of genes. eBAC automatically locates and analyzes the BACs containing the genes of interest, finds the appropriate homology arms and designs all necessary primers for BAC engineering as well as tests the BAC for critical restriction sites. eBAC shortens the time for designing BAC recombination from many hours to seconds.