Background: Amoebiasis is a parasitic disease caused by the intestinal protozoon Entamoeba histolytica. Microscopic examination fails to differentiate E. histolytica from the morphologically identical nonpathogenic Entamoeba dispar. To avoid unnecessary treatment of individuals infected with nonpathogenic E. dispar, it is essential to differentially diagnose infections caused by pathogenic from nonpathogenic Entamoeba spp. Objective: The aim of this study was to assess the efficacy of nested multiplex PCR (NM PCR) technique as a diagnostic method for differentiating infections caused by E. histolytica and E. dispar. Materials and methods: Stool samples collected from patients with and without symptoms of amoebiasis were screened for E. histolytica/E. dispar trophozoites/cysts by microscopic examination. NM PCR was performed on a total of 52 samples targeting the genus-specific 16S-like ribosomal RNA gene for simultaneous, differential detection of E. histolytica and E. dispar. Results: NM PCR detected E. histolytica at 439 bp and E. dispar at 174 bp, and it was positive in 31 out of 32 cases with a sensitivity of 96.85%. From those, 17 (32.7%) samples were positive for E. histolytica, 12 (23.1%) for E. dispar, and three (5.7%) for both species. In addition, NM PCR diagnosed E. dispar in one of the negative controls with a specificity of 95%. Conclusions: NM PCR is useful for the specific detection of E. histolytica and E. dispar in stool samples. Additional methods for species differentiation have been used to avoid unnecessary treatment of individuals infected with the nonpathogenic species [12]. PCR demonstrated excellent sensitivity and specificity