BACKGROUND: The cis-AB is a very rare phenotype in the ABO blood group system. It corresponds to a special ABO allele that encodes glycosyltransferase that is capable of synthesizing both A and B antigens. Until now, the exon 6 and 7 gene sequences of cis-AB alleles are well known. In this study, we report on the intron 6 sequence structure of the cis-AB allele. METHODS: Standard serologic tests for the ABO blood group phenotypes were performed in four cis-AB samples. Allele-separation by cloning and subsequent sequencing was carried out. RESULTS: The results showed that intron 6 of cis-AB is almost identical to the A101 allele except for three single nucleotide polymorphisms at nucleotide positions 163, 179 and 662, where the nucleotides of the A101 replace those of B101. CONCLUSION: The intron 6 sequences of cis-AB in Koreans have both A101 and B101 blood group sequences.