A prospective observational study was conducted to determine the prevalence and the clinical impact of intestinal parasitic infections in diarrheal illness among HIV-infected and HIV-uninfected children hospitalized with diarrhea in Bangkok, Thailand. Stool samples were examined for intestinal parasites using a simple smear method, a formalin-ether concentration method, a modified acid-fast stain and a modified trichrome stain. Intestinal parasites (IP) were identified in the stool specimens of 27 of 82 (33%) HIV-infected and 12 of 80 (15%) HIV-uninfected children (p=0.01). Microsporidia and Cryptosporidium were the most common IP found. Eighty-two percent of HIV-infected and 97% of HIV-uninfected groups presented with acute diarrhea and 76% of each group had watery diarrhea. Pneumonia was the most common concurrent illness, found in 22%. Clinical findings were unable to differentiate children infected with IP. Sixty-three percent of HIV-infected and 83% of HIV-uninfected children who had IP made a satisfactory recovery without specific anti-parasitic therapy. However, 9 children (7 HIV-infected and 2 HIV-uninfected) with persistent diarrhea who also had cryptosporidiosis and/or microsporidiosis did not respond to azithromycin and/or albendazole respectively. HIV-infected children with cryptosporidiosis were older and had more advanced HIV infection than those with microsporidiosis. Routine stool examination for IP should be considered due to the absence of clinical markers. The lack of effective therapy for the major IP found underscores the importance of preventive measures.