Diagnosis of amebiasis by microscopic identification of the parasite in stool is insensitive and unable to distinguish the invasive parasite Entamoeba histolytica from the commensal parasite E. dispar. In this study, we have compared the TechLab E. histolytica-specific antigen detection test with a PCR technique for detection of E. histolytica, and with isoenzyme analysis of cultured amebae. The nested PCR test is based on amplification of the multi-copy small subunit ribosomal RNA gene of E. histolytica and E. dispar. PCR and antigen detection had comparable sensitivities when performed directly on fresh stool specimens, identifying 87% (46/53) and 85% (45/53) respectively of E. histolytica infections identified by isoenzyme analysis. The correlation of antigen detection with PCR for identification of E. histolytica in stool was 93% (45/48). In conclusion all three techniques for specific identification of E. histolytica in fresh stool showed excellent correlation. Only the TechLab E. histolytica antigen detection test was both rapid and technically simple.