Introduction: A cross-sectional study was carried out to assess the prevalence of E. histolytica and E. dispar by examining stool samples obtained from 1,003 students of public schools in Maceió, Alagoas, Brazil. Methodology: All stool samples were processed using the spontaneous sedimentation technique and examined microscopically for the presence of Entamoeba species. In order to distinguish infections caused by E. histolytica, fecal samples presenting cysts of Entamoeba were subjected to specific enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR). Results: The analysis of the fecal specimens by microscopy identified 6.4% (64/1,003) students positive for E. histolytica/E. dispar/E. moshkovskii cysts. The prevalence of E. histolytica detected by ELISA was 3.0% (30/1,003) and by PCR 2.8% (28/1,003), but the difference is not statistically significant (p > 0.05). The prevalence of E. dispar in schoolchildren was 5.0% (50/1,003). Mixed infections with E. histolytica and E. dispar were also detected by PCR. Even though immunological and molecular methods have shown similar results for identification of E. histolytica, ELISA is advantageous over the PCR since it is relatively cheaper and easier to perform. Conclusions: Our study demonstrated the occurrence of E. histolytica in Maceió and highlights the need to introduce a specific diagnostic test to detect amoebiasis cases in public laboratories.