Amoebiasis is one of the major health concerns in manydeveloping countries because it presents one of the three mostcommon causes of death from parasitic disease.The aim of the present work is detection and differentiationbetween morphologically identical but genetically distinct E.histolyica and E. dispar by nested PCR in stool samples.Stool samples were collected from 250 individuals attendingout patient clinic in National Hepatology and Tropical MedicineInstitute in Cairo. They all examined microscopically fordetection of Entamoeba species infection. Only 75 cases wereselected to be tested by PCR.Sensitivity and specificity of nested PCR assay is reportedas 100% and 73.3% respectively for detection anddifferentiation between Entamoeba species.From the present study, it can be concluded that PCR areconsidered to be adequate diagnostic tools used to distinguishbetween E. histolytica and E. dispar to avoid unnecessary andpossibly harmful therapies.