Neurons expressing the m1, m2, and m4 muscarinic receptor genes in the adult rat striatum were identified and characterized by using several in situ hybridization and immunohistochemical procedures. Combined in situ hybridization for the simultaneous detection of two mRNAs in the same section or in adjacent sections as well as in situ hybridization and immunohistochemistry on adjacent sections permitted us to identify the neurons containing m1, m2, or m4 receptor mRNA. Our observations demonstrate that m1, m2, and m4 receptor genes are expressed in one or several phenotypically distinct neuronal populations. The m1 receptor gene was the most widely expressed (85% of the striatal neurons). Most cholinergic neurons (80% or more) contain m1, m2, and m4 receptor mRNAs. Almost all the substance P neurons contain m1 and m4 receptor mRNA. All enkephalinergic neurons contained m1 receptor mRNA, but only 39% contained m4 receptor mRNA. Most somatostatin and neurotensin neurons expressed the m1 receptor gene, but only a few (15% and 9%, respectively) contained m4 receptor mRNA. The present study offers anatomical evidence that ACh may act directly in complex ways on the main neuronal populations of the striatum through muscarinic receptors. The m1, m2, and m4 receptors may act as autoreceptors to control ACh release and possibly other parameters of ACh neurons. On the other hand, the m1 and m4 receptors may act as heteroreceptors in cholinoceptive efferent neurons (enkephalin and substance P neurons) and other neurons (somatostatin/neuropeptide Y and neurotensin neurons). The presence of m4 receptor mRNA in only parts of the enkephalin, somatostatin, and neurotensin neuronal populations indicates that muscarinic receptor gene expression contributes to the functional and anatomical heterogeneity of the striatum that may relate to higher order of organization, including patch-matrix compartmentalization. The wide expression of m1 and m4 receptor genes in the striatum suggests that ACh may directly influence neurotransmitter release and synthesis in striatal efferent and intrinsic neurons. Our results imply that the specific pattern of expression of the muscarinic receptor genes mediates direct effects of ACh on activities and functions of chemically and topologically defined striatal neuronal populations. Since the expression of muscarinic receptors occurred in the three main neuronal populations of the striatum, namely ACh, enkephalins, and substance P neurons that also express dopamine receptors, it is highly probable that ACh and dopamine may act together at the single-cell level to influence striatal functions.