Differentiation between E. histolytica and non pathogenic species as Entamoebadispar, which are morphologically identical species, is essential for rapid treatment decision, precaution of the invasive disease and public health. This study evaluated the real time PCR for detection of intestinal amoebiasis in comparison with microscopic examination. Stool samples were obtained from symptomatic 40 patients from outpatient clinic of Benha University Hospitals and Benha Educational Hospital. Twenty suffered from dysentery and 20 cases were not suffering dysentery. In addition 10 stool samples of other parasitic infection as Giardia lamblia and Cryptospordiumparvum were examined by direct smear, iodine stained smear, formol ether concentration technique and real time PCR for detection of E. histolytica DNA. Formol ether concentration technique showed that 20 (40%) samples were positive for E. histolytica but real time PCR showed 26 (52%) positivity. All samples positive by microscopy were also positive by PCR and additional 6 PCR positive cases. There was no cross reaction with other parasites as G. lamblia and C. parvum.