Background: Enterocolitis and gastroenteritis remain major health problems, particularly in children living in developing countries. Intestinal protozoa, such as Entamoeba histolytica, Blastocystis, and Cyclospora, are frequently associated with these conditions. Amebic colitis can cause serious complications, including fulminant necrotizing colitis, toxic megacolon, extraintestinal amebiasis, and stunting in children. The diagnosis of amoebiasis is challenging, relying on microscopic examination, which cannot distinguish E. histolytica from the nonpathogenic E. dispar and E. moshkovskii. Therefore, this study aimed to identify intestinal parasites, particularly Entamoeba, their prevalence, and the clinical characteristics of patients admitted for enterocolitis and gastroenteritis at a tertiary-referral hospital.Material and Methods: A cross-sectional, retrospective study was conducted at a national, tertiary-referral government hospital, in Jakarta. Of the 111 retrieved medical records from hospitalized patients with enterocolitis and gastroenteritis, for which parasitology feces were examined, 54 fecal samples (48.6%) were still available in the parasitology laboratory storage. All fecal samples underwent the following tests: 1) direct stool examination, after staining with 1% Lugol’s solution, and using the water–ether concentration method; 2) modified acid-fast staining for coccidian parasites; 3) Jones’ culture medium to detect Blastocystis; 4) copro-antigen assay to detect Cryptosporidium and Giardia; and 5) a polymerase chain reaction (PCR) assay to identify Entamoeba. Clinical and demographic data were obtained from the medical records. Results: Largely, patients (44.1%) were from the cohort of young children ≤5 years old, followed by adults aged 19–60 years old (24.3%). Both cohorts exhibited polyparasitism. Intestinal parasites were detected in 17 out of the 54 samples (31.4%). These included 6 (11.1%), 2 (3.7%),5 (9.2%), 3 (5.5%), 2 (3.7%), and 1 (1.8%) samples that were positive for Blastocystis, E dispar, E. histolytica, E. moshkovskii, Cryptosporidium, and Dientamoeba fragilis, respectively. PCR analysis revealed that 10 samples were positive for Entamoeba infection, eight of which originated from pediatric patients. Conclusion At a national tertiary-referral hospital in Indonesia, Entamoeba infection was the most prevalent parasite among pediatric patients with enterocolitis. E. histolytica and E. moshkovskii were the two main species identified by PCR. Therefore, PCR assays and fecal occult–blood tests are recommended in cases of enterocolitis and gastroenteritis.