The gene responsible for the neuromuscular disease idiopathic torsion dystonia (DYT1) has recently been mapped to human chromosome 9q32-34. Our goal is to identify candidate genes for torsion dystonia as well as other neurologically important genes in this region. To accomplish this we have characterized the expression patterns of transcribed sequences identified within a collection of 3000 human 9q32-34-specific clones. Screening of this clone collection with cDNA probes from various brain and peripheral tissues resulted in the identification of 143 clones corresponding to 9q32-34-specific transcripts. Thirty three of these corresponded to transcripts expressed in a brain-specific manner and thus represent preferred candidates for the dystonia gene. None of these candidates were expressed specifically in the putative dystonia target tissue, basal ganglia. The 9q32-34 collection was screened with a subtracted probe enriched in striatal sequences using a directional tag PCR subtraction method. This resulted in the identification of several genes exhibiting preferential expression in the striatum as compared to cerebellum.