As next generation sequencing and microarray analysis become less expensive and easier to access, the most difficult aspect of genomics projects is no longer generating the data itself, rather it is extracting biological meaning from the data. We contend that this aspect of data analysis, especially the limited databases available for the powerful technique of gene set enrichment analysis, is becoming the major roadblock to bench scientists producing research outputs from genomics experiments. While there are existing gene annotation and gene set enrichment tools, most are relatively narrow in the databases they cover and they therefore frequently 'miss' biologically important observations. For this reason, we have generated GeneSetDB, a comprehensive meta-database with associated gene set enrichment analysis statistical tools, which integrates a large number of other biological databases (see Source DB) for gene set analysis.