A number of DNA probes which hybridize to highly abundant DNA sequences of Entamoeba histolytica were developed. Variations in the hybridization patterns of different E. histolytica strains were detected with selected probes. Four types of restriction fragment length patterns were obtained. Of these, the first class belonged to E. invadens and E. histolytica-like var. Laredo. The next two classes consisted of various strains of E. histolytica which were originally isolated from symptomatic patients and possessed pathogenic patterns of isoenzymes (zymodemes), whereas the fourth group contained E. histolytica strains with nonpathogenic zymodemes obtained from asymptomatic carriers. DNA probes, based on DNA sequences specific to E. histolytica isolates with pathogenic and nonpathogenic zymodemes were isolated, and their nucleotide sequences were determined. These probes (P145 and B133) hybridized selectively to DNA of isolates possessing either pathogenic or nonpathogenic isoenzyme patterns. The newly developed probes could be useful for diagnostic purposes and could serve as tools to investigate the molecular basis of pathogenicity and the genetic mechanisms which regulate the variable aggressive behavior of the parasite.