Huntington's disease (HD) is an inherited neurodegenerative disorder expressed when a trinucleotide repeat in the gene IT-15 is expanded. The mechanism by which the expanded repeat causes the expression of the disease is unknown. Possible mechanisms include alterations in the amount of the mRNA, potentially resulting from changes in gene transcription or abnormal mRNA stability. In order to determine whether the expanded IT-15 allele is present in mRNA, we isolated total RNA from the cortex and striatum of patients and controls. To distinguish the two alleles of the IT-15 transcript in HD patients, we amplified across a region containing a dimorphic single triplet deletion observed on some chromosomes and found that the relative intensity of the two PCR bands amplified from genomic DNA and those amplified from first strand cDNA from brain tissue were essentially equal. In order to determine whether the exon containing the expanded CAG repeat is present in IT-15 mRNA from HD patients, we amplified across this region and demonstrated the presence of the expanded repeat in cDNA from both striatum and cortex. Based on this evidence, we suggest that the mechanism of disease expression does not occur during transcription or in the stability of the RNA, but rather occurs during translation or postranslationally.