We evaluated the colorimetric polymerase chain reaction (PCR)-based method for the detection and differentiation of Entamoeba spp. and compared the efficacy of E. histolytica-specific antigen detection in faeces with the detection of specific antibodies to E. histolytica-specific antigen in faeces, by enzyme-linked immunosorbent assay. Faecal samples were obtained from patients attending hospital in Chandigarh, India, from March 2001 to February 2002. The PCR-based colorimetric method was found to be the most sensitive (100%) and it could differentiate between pathogenic and non-pathogenic Entamoeba spp. The present study also emphasized that the antigen detection system may prove to be a better diagnostic tool than the antibody detection system in endemic areas.