Because the expression levels of housekeeping genes are relatively constant in most tissues, they are often useful controls when quantifying gene expression. We present an analytical method for identifying candidate housekeeping controls using expressed sequence tags (ESTs) from The Institute for Genomic Research Tomato Gene Index. We found relative expression levels for a collection of 127 transcripts and calculated the percentage of cDNA libraries that had expression levels (for a given transcript) within 2-fold through 10-fold ranges. When all libraries were considered together, the highest ranked housekeeping controls included transcripts for a DanJ-like protein, translationally controlled tumor protein, two alpha-tubulins, cyclophilin, and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). For each organ (leaf, root, fruit, and flower), at least one transcript was found that occurred within a 2-fold range of expression in all respective libraries. These included transcripts for alpha-tubulin, DnaJ-like proteins, phosphoglycerate kinase, and GAPDH, although different transcripts appear better suited than others for different tissues. This analytical method is useful for identifying candidate housekeeping controls in particular tissues and at particular levels of expression and would be relevant for any species for which significant EST data exist.