Serine-threonine protein kinases in the ribosomal S6 kinase (rsk or p90rsk) family have been implicated as signaling intermediates in the cellular response to several growth factors. To investigate the molecular diversity of human p90rsk isoforms, mixed degenerate oligonucleotide polymerase chain reaction was used to isolate partial rsk cDNAs (1.1 kb). Three closely related human rsk cDNAs were obtained (HU-1, HU-2, HU-3). These cDNAs are encoded by separate genes based on DNA sequence diversity and distinct patterns seen with genomic Southern blots. Northern analysis revealed different sized mRNA transcripts for each isoform. A full-length HU-1 cDNA (3.1 kb) was subsequently isolated from a HeLa cell library. 5'-cDNA clones for HU-2 and HU-3 were isolated using the "rapid amplification of cDNA ends" strategy. Experiments using human x hamster somatic cell hybrids localized the HU-1 gene to human chromosome 3; HU-2 is on chromosome 6; and HU-3 is on the X chromosome. The tissue distribution of human rsk mRNAs was determined using ribonuclease protection assays. HU-3 mRNA was present in multiple RNA samples. HU-2 was expressed in fibroblast > muscle > lymphocyte = placenta > liver. HU-1 was expressed in Epstein-Barr virus lymphocyte > > muscle = liver > fat = placenta. These results indicate that the multiplicity of p90rsk isoforms is increased to at least three for humans and that marked tissue-/cell-specific differences in p90rsk isoform expression are present.