In order to clarify the reported discrepancies in S100-alpha protein and mRNA distribution in rat tissues, a rat S100-alpha cDNA has been isolated and this species homologous probe along with a rat S100-beta cDNA probe has been used to examine S100 mRNA expression in rat tissues. Although the rat S100-alpha cDNA was missing approximately 30 nucleotides of coding sequence, only 4 conservative changes in amino acid sequence were observed when the deduced amino acid sequence was compared to the bovine S100-alpha amino acid sequence. Thus, S100-alpha proteins, like S100-beta proteins, are highly conserved among species. All nineteen of the tissues examined (including cerebrum and cerebellum) contained S100-alpha mRNA. In addition, S100-beta mRNA was detected in thirteen of the nineteen tissues examined. These results are in agreement with previous protein distribution studies and further demonstrate that S100 proteins are not brain-specific and are expressed in a large number of tissues. Although S100-alpha and S100-beta mRNAs were detected in rat tissues which had previously been reported to contain S100-alpha and S100-beta protein, a direct correlation between the protein and mRNA levels were not observed, suggesting that different mechanisms regulate S100 expression in various tissues. S100-alpha exhibited a single similar size mRNA species (0.5 Kb) in all tissues examined, as did S100-beta (1.5 Kb), suggesting that the individual S100 proteins are expressed as single mRNA and protein products in rat tissues.