We used the polymerase chain reaction (PCR) to study the distribution of Entamoeba histolytica and E. dispar in 1,872 individuals in 14 communities in the northern Philippines. Here we report a field study using a DNA extraction protocol from formalin-fixed stool specimens as previously reported. This assay detected 137 stools (7.318%) containing E. dispar and 18 stools (0.961%) containing E. histolytica. The most affected age group for E. histolytica/E. dispar infections were those 5-14 years of age. There was no significant difference in the sex distribution of E. histolytica, while in the case of E. dispar, a higher prevalence was observed in females (9.186%) than in males (5.731%) (P < 0.01). An apparent clustering of stool-positive cases of E. histolytica and E. dispar was also observed in the northern part of the study area. The results of this survey demonstrate that E. dispar is highly prevalent in the communities studied. Moreover, it offers promise for the PCR using DNA extracted from formalin-fixed stools as a sensitive epidemiologic tool for detecting E. histolytica and E. dispar infections.