Objective To investigate the single nucleotide polymorphisms (SNPS) in the coding regions of the human ABCA2 gene and to determine the association of some of these SNPs with gallstone disease in a Chinese population. Methods The exons and part of the introns of the ABCA2 gene were sequenced using a fluorescent labeling automatic method in 24 patients with gallstone disease to identify and characterize the SNPs in a Chinese population. For SNPs in the exons, case-control studies were performed on patients and controls. Results Twelve SNPs were found within a 16911 bp region of the ABCA2 gene. Among them, two were in the exons, ten in the introns and five were novel SNPs. There was no significant difference in the SNPs genotype between the patients and the controis. Conclusions There is an important ethnic difference in the SNPs distribution of the human ABCA2 gene. The distribution of SNPs in the coding regions of the human ABCA2 gene is not significantly different between the patients and the controls.