Trehalase is the least studied of the membrane-bound alpha- glucosidase enzymes. Here we report the isolation and characterization of the mouse trehalase (Treh) gene. Initially, PCR using primers based on published rat cDNA sequence was used to clone a partial mouse cDNA. This allowed design of mouse primers which identified a single positive clone in a bacterial artificial chromosome (BAC) library of mouse genomic DNA. Analysis of BAC subclones showed that the Treh structural gene spans approximately 13 kb and comprises 15 exons. Data from genomic Southern blotting were consistent with mouse Treh being a single copy gene. The transcription initiation site was determined by both S1 nuclease mapping and 5' rapid amplification of cDNA ends (5' RACE) to be located 25 nt upstream of the ATG in exon 1. The mouse Treh exons were found to have an open reading frame of 1728 nt and the encoded protein of 576 amino acids showed 81, 82 and 93% amino acid sequence identity with rabbit, human and rat trehalase, respectively. The trehalase signature sequence found at amino acids 162 to 175 had 100% identity with the corresponding region of rabbit, human and rat and 79% identity with that for yeast trehalase. When a mouse Treh cDNA was used for Northern blot analysis of RNA from 12 mouse tissues, Treh mRNA expression was detected only in kidney and small intestine. The size of the mRNA in both of these tissues was estimated to be approximately 2.1 kb, furthermore both tissues appear to have the same transcription initiation site as determined by nuclease protection. Using the T31 radiation hybrid panel, mouse Treh was shown to be located on Chromosome 9 in a broad region that is orthologous with human Chromosome 11q23. The human trehalase gene (TREH) was identified in the latter location via database searching, which also revealed the overall structure of the human gene as being similar to that of the mouse.