The occurrence of diarrhea in children under five years old (toddlers) is still a serious health problem because it can cause mortality and malnutrition in children. Diarrhea is one of the biggest causes of death in toddlers in the world. Data from the World Health Organization (WHO) reports that more than 10 million children under five years old die every year and around 20 percent of them die because of diarrhea. One etiology of diarrhea infection in children under five years old who often escapes attention is diarrhea caused by parasites. As a developing and tropical country, the incidence of diarrhea due to parasitic infections in Indonesia is quite high. Examination of diarrhea samples in children under five years old to identify the type of parasites that play a role in the incidence of diarrhea. Stool samples were collected from patients seeking treatment at several primary health care and hospitals in Jakarta, Banjarmasin and Makassar during 2015-2016. The stool specimens were collected in containers containing formaldehyde for microscopic examination. Blastocystis hominis was found to be the most prevalent parasite with an infection rate of 12.46% followed by Entamoeba coli 1.73%, Ascaris lumbrichoides 0.35%, Oxiuris vermicularis 0.35%, Endolomax nana 0.35%, and Hookworm (Ancylostoma sp and Necator americanus) 0.35%. Parasitic diarrhea increases susceptibility to other infections, should not be neglected, particularly in patients with chronic diarrhea. Accurate diagnosis decreases morbidity and mortality in patients with parasite infection.