Background: The genus Entamoeba contains many species. E. histolytica is the causative agent of amoebiasis while others are non pathogenic. The main morphological characteristics of the trophozoite and cyst stages are important for precise microscopic diagnosis and differentiation of amoebae. Objectives: The present study was designed to determine the proportion of infection with the different intestinal amoebae and to describe the main morphological characteristics for precise microscopic diagnosis. Materials and methods: This study was conducted on 200 faecal specimens collected from patients attending outpatients clinics of Cairo University Hospital. Out of these samples, 100 were from patients suffering from different gastrointestinal manifestations and 100 from patients free from GIT manifestations. All samples were examined for intestinal amoebae microscopically using eosin, iodine, Lactophenol cotton blue (LPCB) and trichrome stains and confirmed using micrometry. Results: In the present study, microscopic examination using eosin, iodine, LPCB and trichrome stains demonstrated that proportion of infection with different intestinal amoebae was 3.5%. Using trichrome stain, cytoplasm of the trophozoite was red and sometimes with a tinge of purple while nuclei and karyosome were dark red. Cyst wall was purple and cytoplasm was dark red with less contrast with the nuclei. Conclusion: Precise microscopic examination helps to determine the true prevalence of different types of intestinal amoebae. PVA is suitable for long term storage. LPCB is a good and easy screening method. WT staining procedure was processed in about 6 steps that took approximately 30 min.