A total of 450 stool samples were collected from inpatient and outpatient clinics of Pediatric Department, Minia University Hospital, Minia District, Egypt. Two groups of patients were studied, including 200 immunosuppressed and 250 immunocompetent children. Stool samples were subjected to wet saline and iodine mounts. A concentration technique (formol-ether sedimentation method) was carried out for stool samples diagnosed negative by wet saline and iodine mounts. Samples were stained by 2 different methods; acid fast stain (modified Ziehl-Neelsen stain) and Giemsa stain. Total 188 cases (94%) were diagnosed positive for parasitic infections among immunosuppressed children, whereas 150 cases (60%) were positive in immunocompetent children ($P$<0.0001). The most common protozoan infection in immunosuppressed group was $Cryptosporidium$ $parvum$ (60.2%), followed by $Blastocystis$ $hominis$ (12.1%), $Isospora$ $belli$ (9.7%), and $Cyclospora$ $caytenensis$ (7.8%). On the other hand, $Entamoeba$ $histolytica$ (24.6%) and $Giardia$ $lamblia$ (17.6%) were more common than other protozoans in immunocompetent children.