The murine testis transcriptome (MTT) represents a database of all genes currently known to be expressed in the murine testis, and will used to construct high density cDNA arrays for toxicogenomic analyses. The NCBI UniGene, Jackson Laboratories Mouse Gene Expression (GXD), and National Library of Medicine (MEDLINE) databases were searched to identify genes expressed in mouse testicular tissue. By combining these publicly available data, it was possible to create a more comprehensive MTT than by using any of these sources exclusively. 1767 known genes were identified. 1164 (66%) were obtained from the UniGene database as clusters containing ESTs sequenced in libraries derived from murine testis. Analysis of the GXD and MEDLINE for genes expressed in the testis or component cell types identified an additional 335 (19%) and 268 (15%) genes, respectively. In addition to identifying genes experimentally determined to be expressed in the murine testis, the search of the literature also identified genes known to be involved in testis function in humans or rats, resulting in the selection of a significant number of homologous genes in the murine databases that would not have otherwise been included in the MTT. Of these 268 genes, 151 (56%) were derived from mouse, 98 (37%) were derived from rat, and the remaining nine (4%) were derived from human model systems. Gene expression analysis of 588 genes using a commercially available array identified 171 genes expressed at high levels in murine testis. Of these 171, 107 (63%) were already contained in the MTT. The remaining 64 (37%) were added to the MTT, bringing the final total of known genes in the MTT to 1831 (www.bch.msu.edu/~zacharet/MTT.htm). This approach represents an inexpensive, efficient, and productive method for creating comprehensive cell type, tissue, or organism specific transcriptomes, and takes full advantage of the exhaustive cDNA sequencing efforts of other researchers.