Huntington's disease (HD) is associated with an expanded and unstable (CAG) > 35 repeat within a gene of unknown function. We isolated the complete coding region of the rat HD gene (rhd) from cDNA libraries and investigated its expression in different developmental stages of rodent tissues. The rat gene exhibits 90% peptide sequence identity to the human and 96% to the murine sequence. The (CAG)n repeat is markedly reduced in the rat compared to the average human (CAG)n block. Northern blot analysis and in situ hybridizations reveal that in rodents the hd gene is already expressed during embryonal development. As in humans, the rhd gene is expressed in two transcriptional isoforms which result from different polyadenylation signals. In mice, however, a third transcript of intermediate size was found predominantly expressed in brain. This transcript is downregulated in later development. At day 14.5 p.c. the level of rhd expression is similar in the brain and in non-neuronal tissues. In contrast, the expression in non-neuronal tissues is markedly reduced in adult animals and corresponds to the restricted distribution of neuropathologic changes observed in HD patients.