Diarrhea is responsible for high morbidity and mortality among children under the age of five in developing countries. Poor diet and unsafe water supply in households contributes to the prevalence of diarrhea. This study was carried out to determine intestinal parasitic protozoa causing diarrhea. Participants were children under-five years attending Municipal hospitals in Dar Es Salaam with either acute or chronic diarrhea. A total of 720 stool samples were analyzed. Parasitic protozoa were investigated by standard microscopy and PCR methods. The highest prevalence of diarrhea (29.6%) was found in the age groups of 12-23 months, followed by 24-60 months (15.6%), 6-11 months (8%) and least 0-5 months (2.4%). Microscopic method identified 41% parasitic protozoa, PCR 55.6%. However, m-PCR was more discriminative and sensitive, such that the 144 samples identified microscopically as E. histolytica, were differentiated as; E. histolytica 48 (33.3%), E. dispar 80 (55.6%) and E. moshkovskii 16 (11.1%). The most common protozoa were Giardia lamblia 35.6 % (256), followed by Entamoeba histolytica 12.2% (88), Cryptosporidium parvum 7.8 % (56), and Helminthes 12.7% (92). PCR methods should be advocated for differential diagnosis of parasitic causes of diarrhea in Tanzania for children.