Huntington's disease (HD) is caused by the inheritance of a copy of the gene encoding mutant huntingtin with an expanded CAG repeat. Phosphodiesterase 10A (PDE10A) mRNA decreases in transgenic HD mice expressing exon 1 of the human huntingtin gene (HD). The mouse PDE10A mRNA is expressed through alternative splicing and polyadenylation in a tissue-specific manner and that transcription of striatal PDE10A mRNA is driven by two promoters. PDE10A2 is the predominant isoform of the gene is expressed in the striatum. Using in situ hybridization and quantitative RT-PCR, we determined that decreased steady-state levels of PDE10A2 mRNA were caused by an altered transcription initiation rate rather than by post-transcriptional mRNA instability in HD mice. Transcription from three initiation sites located within a 50-bp region in the PDE10A2-specific promoter was differentially affected by the presence of the mutant huntingtin transgene. The mouse and human PDE10A2 promoters are highly conserved with respect to the relative position of cis-regulatory elements. Several transcription factors that have been shown to interact with mutant huntingtin, including Sp1, neuron restrictive silencing factor, TATA-binding protein and cAMP-response element binding protein, are unlikely to be involved in mutant huntingtin-induced PDE10A2 transcriptional dysregulation.