We isolated nearly full-length clones of S-100 alpha and beta subunit cDNAs from a human brain cDNA library. The alpha subunit cDNA was 579 bp long and contained 99 bp of 5'-noncoding region, 282 bp of coding region, and 198 bp of 3'-noncoding region. The beta subunit cDNA was 743 bp long and contained 57 bp of 5'-noncoding region, 276 bp of coding region, and 410 bp of 3'-noncoding region. An amino acid sequence comparison between human and bovine alpha subunits and between human and rat beta subunits showed that both subunits were nearly entirely conserved. The amino acid sequences of human alpha and beta subunits were conserved at both Ca(2+)-binding domains. Northern blot analysis of brain RNA showed that human alpha and beta subunit cDNA probes discriminated between alpha and beta subunit mRNAs. By using these subunit-specific cDNA probes, it was demonstrated that alpha and beta subunit mRNAs were expressed in different manners among tumor cell lines: beta was detected in melanoma and some glioma cell lines, while alpha was detected only in a melanoma cell line. Southern blot analysis showed that there were no major deletions and rearrangements of alpha and beta subunit genes in these cell lines, regardless of the level of alpha and beta subunit expression, suggesting that the expression of these subunits may be regulated at the transcriptional or RNA stability level.