Background: Parasitic gastrointestinal infections have been variably reported among immunocompromised adults while data on children have been limited. This prospective cross-sectional study aimed to assess the clinical profile of intestinal parasitic infections among immunocompromised children with diarrhoea and their treatment response. Methodology: Two freshly voided stool samples taken for two consecutive days were examined by direct and formalin-ether concentrated smears. Modified Ziehl-Neelsen staining was used to detect Cryptosporidium, Isospora belli, and Cyclospora cayetanensis. Blastocystis hominis was identified using in vitro culture. Subjects positive for stool parasite(s) received standard therapy according to the aetiology and were evaluated afterward. Results: Forty-two subjects from Jakarta, Indonesia were included in this study, mostly aged one to five years (78%) and HIV infected (52%). Parasites were found in 24/42 (57%) subjects in which B. hominis comprised the largest proportion (23/24 = 96%). Cryptosporidium was identified in two subjects who were HIV infected with CD4 percentages of < 15%. No helminth infestations were found. Parasites were most frequently found in preschool age children (16/23), in those with recurrent or watery diarrhoea (23/24 and 14/18, respectively), and in HIV subjects not receiving antiretrovirals (16/22). Of 13 subjects evaluated for response to a 10-day metronidazole course for B. hominis infection, seven achieved clinical remission and nine had their parasites eradicated. Conclusions: The prevalence of intestinal parasitic infection in immunocompromised children with persistent and/or recurrent diarrhoea is moderately high and dominated by B. hominis infection. Clinical remission and parasite eradication can be achieved in B. hominis infection treated with metronidazole. © 2010 Idris et al.