DNA from five isolates of Entamoeba histolytica were examined for their pathogenicity by polymerase chain reaction. Three isolates SH-3,SH-6,SH-8 were isolated from patients with acute amoebic dysentery, whereas SH-5 and SH-7 were isolated from asymptomatic cyst passers. Gel electrophoresis of PCR products showed that primers P11, P12 for pathogenic strains could amplify genomic DNA extracted from SH-8, and primers P13, P14 for nonpathogenic strains could amplify genomic DNA extracted from SH-3,SH-5,SH-6 and SH-7. Furthermore, zymodeme analysis and the reactivity of McAb 4G6, which recognizes the 30 kDa antigen of pathogenic E. histolytica indicated that only SH-8 was pathogenic, while the others were nonpathogenic. The results of the genotypic analysis by PCR were in accord with the phenotypic properties. It is suggested that there are differences in genomic DNA between pathogenic and nonpathogenic strains. PCR is a highly sensitive and specific method for genomic DNA analysis of E. histolytica.