Intestinal microsporidiosis is a common opportunistic disease associated with diarrhea in adult AIDS patients in Thailand; the data regarding this infection in children are scarce. The present study was designed to investigate the prevalence and clinical features of intestinal microsporidiosis in hospitalized HIV-infected and uninfected (free of HIV) children with diarrhea. Of the 95 HIV-infected children and 87 uninfected children, 24 (25.3%) and 13 (14.9%) respectively were diagnosed with intestinal microsporidiosis. Species identification of microsporidia spores, by transmission electron microscopy, demonstrated Enterocytozoon bieneusi in 5 cases. Cryptosporidium parvum was a common coinfective parasite; pneumonia was the most frequent concurrent disease found in children with intestinal microsporidiosis. Malnutrition was commoner in the HIV-infected group (79.2% vs 23.1%; p = 0.003). This study indicates that intestinal microsporidiosis is an important disease in both HIV-infected and uninfected Thai children with diarrhea.