Infection with pathogenic intestinal protozoa as Giardia lamblia, Entamoeba histolytica and Cryptosporidium parvum cause considerable gastrointestinal morbidity, malnutrition and mortality worldwide, especially among young children in developing countries. The present study was carried out on 71 cases (44 males & 27 females) chosen from Pediatric and Internal Medicine Inpatient and Outpatient Clinics of Zagazig University Hospitals, complaining of different gastrointestinal troubles with an age range of 6-60 years. Also, 20 apparently healthy individuals (11 males & 9 females) cross matched were considered as a control negative group. All stool samples were examined by direct wet smears, concentration techniques, staining of the smears using trichrome stain and Modified Ziehl-Neelsen method. Copro-antigen detection in faecal sample was by using quick immunochromatographic test. A total of 71 cases suffering from different GIT manifestations showed G. lamblia (30.7%), Cryptosporidium parvum (19.8%), Entamoebahistolytica/E. dispar (11%) and mixed infection of three protozoa (6.6%). However, by copro-antigen G. lamblia was positive in (31.8%) of C. parvum in (20.9%); E. histolytica/E. dispar in (11%) of cases. Immunochromatography/copro-antigen test recorded sensitivity and specificity of (100%) and (96.6%) respectively in G. lamblia detection. For C. parvum, sensitivity was (100%) and specificity was (97.1%) while for E. histolytica/E. dispar, sensitivity and specificity were (100%) for both. Immunochromatographic assay proved to be simple, easy and useful in confirming absence or the presence of intestinal protozoan infection in clinically suspected cases with negative stool examination.