This study was designed to reveal the association between the polymorphism of cholesteryl ester transfer protein (CETP) gene loci and gallbladder stone disease. By means of polymerase chain reaction (PCR) and restriction fragment length polymorphisms (RFLEs) of CETP taqIB, BamHI genes were examined in 104 patients subjected to cholecystectomy for symptomatic gallstone disease and 68 healthy controls. The distribution of CETP taqIB polymorphism in the patients with gallstones differed significantly from that of the controls. The B1 allele and B1B1 jects were more frequently revealed in patients with gallstones (0.523, vs 0.346, 0.288 vs 0.1176, P < 0.05). The B2 allele and the B2B2 jects appeared in the controls more frequently (0.654 vs 0.477, 0.4264 vs 0.242, P < 0.05). The H1 allele, H2 allele and H1H1 genotypic, H2H2 genotypic frequencies of the patients with gallstones were not significantly different from those of the controls (P > 0.05). The results suggest that B1 allele is the major gene in the patients with gallstones, and B2 allele is more frequently revealed in the controls.