To establish a fast, simple and solid method of studying microsatellite instability (MSI) in gastric cancer, a panel of 12 microsatellite sites, D1S548, D1S552, D5S346, TP53, IGF II R(G)(8), IGF II R(CT)(5), TGFbetaR II(GT)(3), TGFbetaR II(A)(10), hMSH3(A)(8), hMSH6(G)(8), BAX(G)(8) and Bat26, were detected by denatured polyacrymide gel electrophoresis-silver stain in 28 gastric cancers. Bat26 was also analyzed by denatured high performance liquid chromatograph (DHPLC) at 50 degrees in the DNASep Cartridge. Two MSI-H (7.14%) and 15 MSI-L cancers (53.6%) were identified in 28 gastric cancers. Bat26 was positive only in 2 MSI-H cancers. The alterations of Bat26 and MSI-H status were coincident (P<0.01). The two Bat26+ cancers were also confirmed by DHPLC. Results obtained from DHPLC and gel electrophoresis were completely consistent. Thus, DHPLC analysis of Bat26 site may be a favorable method of detecting MSI-H status in gastric cancer, and be of clinical importance.