A prospective study of intestinal microsporidiosis in HIV-positive children was conducted at the Queen Sirikit National Institute of Child Health and Phramongkutklao Hospital, Bangkok, Thailand. Hospitalized HIV-positive children with and without diarrhea were enrolled in this study. Microsporidial spores identified by calcofluor fluorescent and gram-chromotrope stain were confirmed by electron microscopy. As well as Cryptosporidium parvum, Microsporidia was the most common protozoa found in the present study, each was 7.1%. Microsporidia was significantly more common in those who had diarrhea. Intestinal microsporidiosis was found in HIV-positive children with both acute and chronic diarrhea. This study emphasizes the importance of Microsporidia in HIV-infected children. Early detection of microsporidia could be of benefit for the patients, since the infection is treatable.