BACKGROUND: Tourette disorder is characterized by motor hyperactivity and tics that are believed to originate in basal ganglia. Postmortem immunocytochemical analyses previously revealed decreases in cholinergic, parvalbumin, and somatostatin interneurons (IN) within the caudate/putamen of individuals with TS. METHODS: We obtained transcriptome and open chromatin datasets by snRNAseq and snATAC-seq, respectively, from caudate/putamen postmortem specimens of 6 adult TS and 6 matched normal control (NC). Differential gene expression and differential chromatin accessibility analyses were performed in identified cell types. RESULTS: The data reproduced the known cellular composition of the human striatum, including a majority of medium spiny neurons (MSN) and small populations of GABAergic and cholinergic IN. IN were decreased by ∼50% in TS brains, with no difference in other cell types. Differential gene expression analysis suggested that mitochondrial oxidative metabolism in MSN and synaptic adhesion and function in IN were both decreased in TS subjects, while there was activation of immune response in microglia. Gene expression changes correlated with changes in activity of cis-regulatory elements, suggesting a relationship of transcriptomic and regulatory abnormalities in MSN, OL and AST of TS brains. CONCLUSIONS: This initial analysis of the TS basal ganglia transcriptome at the single cell level confirms the loss and synaptic dysfunction of basal ganglia IN, consistent with in vivo basal ganglia hyperactivity. In parallel, oxidative metabolism was decreased in MSN and correlated with activation of microglia cells, attributable at least in part to dysregulated activity of putative enhancers, implicating altered epigenomic regulation in TS.