Somatostatin-containing neurons of the striatum constitute fewer than 5% of the total neuronal population. Their involvement in the feedforward inhibition of the spiny projection neurons, the modulation of other interneurons, and the regulation of regional blood flow indicates that this small population of neurons plays an important role in the processing of information in the striatum. As a first step in developing a quantitative structural framework within which a more rigorous analysis can be made of the functional circuitry of the striatum, we used modern unbiased stereological techniques to make estimates of the total number of neurons expressing mRNA for somatostatin in the striatum of rats. The strategy developed involved the application of the optical fractionator technique to relatively thick tissue sections that were hybridized in situ with a relatively short oligonucleotide probe conjugated to a nonradioactive reporter molecule. The approach is generally applicable to other subpopulations of in situ hybridized cells in other parts of the brain and can provide a link between molecular neurobiology and stereology. The mean total number of neurons on one side of the striatum was estimated to be 21,300. An analysis of the sampling scheme indicated that counting no more than 200 neurons in a systematic sample of not more than 15 sections per individual results in an estimate with a precision that is more than sufficient for comparative and experimental studies. The issues that must be considered when analyzing in situ hybridized tissue with modern stereological methods, the interpretive caveats inherent in the resulting data, and the unique perspectives provided by data like that presented here for striatal somatostatin neurons are discussed.