S100 protein is a widely used immunohistochemical marker for identification of a number of tumors including malignant melanoma and pleomorphic adenoma of the salivary gland. To extend the detection techniques for S100 protein to the level of its mRNA, sections of malignant melanoma and pleomorphic adenoma were hybridized in situ with a 35S-labeled anti-sense RNA probe complementary to the mRNA for the beta subunit of human S100 protein. Both tumors were labeled with the anti-sense RNA probe but not with a sense RNA probe. In addition, sections of normal and tumor tissues which were known not to express S100 protein on the basis of immunohistochemical studies were not labeled with the anti-sense RNA probe. These results established the specificity of the in situ hybridization technique for the detection of S100 protein mRNA. Although most of the tumor cells in both malignant melanoma and pleomorphic adenoma were labeled with the anti-sense RNA probe, unlabeled tumor cells were also present in their vicinity, suggesting there was a heterogeneity among the cells in both tumor types with respect to S100 protein mRNA expression.