A vertical polyacrylamide gradient gel (3% to 7%) was designed to facilitate the electrophoretic resolution and classification of isoenzyme patterns of Entamoeba histolytica isolates. The following enzyme systems were used: phosphoglucomutase (PGM), hexokinase (HX), glucosephosphate isomerase (GPI), and malate dehydrogenase (ME). The modifications in the electrophoretic procedure and sample preparation allowed the reproducible comparison of enzyme patterns of axenic, monoxenic, and mixed cultures of E. histolytica isolated from humans. The clear distinction obtained in gradient polyacrylamide gels, between amebic isoenzyme bands and those from bacteria, renders this technique adequate for application to epidemiological studies where mixed cultures are used. The isoenzyme patterns of eight isolates from asymptomatic carriers, rigorously characterized by the absence of clinical, endoscopic, and serological findings were studied and compared with three well characterized pathogenic strains, cultured under axenic conditions. Our observations confirm the existence of distinct isoenzyme patterns for PGM, HX, and GPI in pathogenic and nonpathogenic strains, and reveal the consistent presence of more than one band for GPI. In addition, a previously undescribed band for GPI with an Rf of 0.64 in a carrier strain was found. The results suggest that while carriers usually harbor amebas with nonpathogenic isoenzyme patterns, pathogenic patterns also may be found in carriers.