Transcription elongation factor S-II stimulates mRNA chain elongation catalyzed by RNA polymerase II. S-II is highly conserved among eukaryotes and is essential for definitive hematopoiesis in mice. In the present study, we report the identification of five novel nucleotide variations in the human S-II gene in the Japanese population. All five variations were located in introns, and no polymorphisms were found in the protein-coding region, suggesting strong negative selection during gene evolution. Together with the SNPs (single nucleotide polymorphisms) reported in the National Center for Biotechnology Information SNP database, our results provide tools for evaluating the role of S-II in complex genetic diseases, such as congenital hematopoietic disorders.