The human UDP-glucuronosyltransferase, UGT1A9, catalyses glucuronidations of various endobiotics and xenobiotics. In the present study, all exons, exon-intron junctions, and the 5'-flanking region (-273 bp) of the UGT1A9 gene in a Japanese subject were sequenced. One base insertion of thymidine in a promoter region of the UGT1A9 gene resulting in A(T)10AT was identified compared to the reference sequence of AF297093 (A(T)9AT). The allele was termed UGT1A9*22. A polymerase chain reaction-single strand conformation polymorphism method was developed to genotype the allele. The allele frequencies of the mutation in 87 Japanese, 50 Caucasian and 50 African-American subjects were 60%, 39% and 44%, respectively. The significance of the polymorphism was investigated by the construction of luciferase reporter plasmids containing 170 bp of the 5'-flanking region of the gene transfected into human hepatoma HepG2 cells. The luciferase activity of the promoter construct containing the A(T)10AT sequence was 2.6-fold higher than that of the construct containing the A(T)9AT sequence. In conclusion, the mutant allele with one base insertion in the promoter region of the UGT1A9 gene would alter the level of enzyme expression and the metabolism of those drugs that are substrates of UGT1A9.