Background: Diagnosis of microsporidiosis is difficult due to its small size needing special stains and identification by an expert. Nowadays, application of polymerase chain reaction (PCR) made diagnosis more sensitive, specific and easier. Objectives: To update the prevalence of intestinal microsporidia and to clarify their genotype patterns in symptomatic and asymptomatic immune compromised and immune competent cases. Patients and Methods: Totally, 323 stool samples were collected and subdivided as 173 from immune compromised (group I) and 150 from immune competent (group II) individuals. Samples were examined for microsporidiosis by light microscopy smears stained by Weber's modified trichrome (WMT) and modified ZiehlNeelsen (MZN), as well as by nested and RFLP PCR techniques. Results: Microsporidial spores were microscopically detected in 45/323 (13.9%) individuals; 25/173 (14.5%) immune compromised and 20/150 (13.3%) immune competent cases. In the two groups, 25/45 (55.6%) were symptomatic complaining of diarrhea, abdominal pain, distension, mal-digestion and weight loss, with statistical significant difference (P<0.001) between infection and presence of symptoms. Nested and RFLP PCR missed only one positive case, thus scoring 97.8% sensitivity and 100% specificity, positive predictive value 100%, negative predictive value 99.6% and diagnostic accuracy 97.8%. In group I, 5 cases were associated with Enterocytozoon (Ent.) bieneusi, 5 with Encephalitozoon (Enc.) species and 15 had mixed infection. In group II, 6 had Ent. bieneusi, 3 had Enc. species and 10 had mixed infection.Sequencing of the internal transcribed spacer of rDNA of five samples demonstrated the Ent. Bieneusi anthroponotic genotype B and the zoonotic potential for genotypes D and K, in addition to one Enc. intestinalis sequence. Conclusion: Prevalence of microsporidiosis was insignificantly higher in immune compromised than immune competent population. Intestinal microsporidiosis can be manifested by different abdominal symptoms or it can be asymptomatic. PCR technique highlighted that mixed infection with Ent. Bieneusi and Encephalitozoon species was the commonest finding among the studied groups. Ent. Bieneusi igenotypes appeared to be related to animal contact and human infection. This, however, could not be accurately defined due to the limited number of available sequences.