Entamoeba moshkovskii cysts are morphologically indistinguishable from those of the disease-causing species E. histolytica and the nonpathogenic E. dispar. Although sporadic cases of human infection with E. moshkovskii have been reported, the organism is considered primarily a free-living amoeba. No simple molecular detection tool is available for diagnosing E. moshkovskii infections. We used polymerase chain reaction (PCR) to detect E. moshkovskii directly in stool. We tested 109 stool specimens from preschool children in Bangladesh by PCR; 17 were positive for E. histolytica (15.6%) and 39 were positive for E. dispar (35.8%). In addition, we found that 23 (21.1%) were positive for E. moshkovskii infection, and 17 (73.9%) of these also carried E. histolytica or E. dispar. The high association of E. moshkovskii with E. histolytica and E. dispar may have obscured its identification in previous studies. The high prevalence found in this study suggests that humans may be a true host for this amoeba.