Background: Microsporidia are a group of obligate intracellular organisms that can infect all animals including man causing disease in both immunocompetent individuals and immunosuppressed patients. The most common microsporidia causing gastrointestinal infection worldwide are Enterocytozoonbieneusi and Encephalitozoonintestinalis.  Objectives: The present study was designed with the aim of estimating the rate of microsporidia in diarrheic children and the evaluation of different staining techniques and nested polymerase chain reaction (PCR) for the clinical diagnosis of intestinal microsporidiosis. Subjects and Methods: One hundred and fifty diarrheic stool samples were collected from Abou El-Rich children hospital laboratory. Samples were examined by “Ryan-Blue" modified trichrome stain (MTS), modified ZiehlNeelsen (MZN), acid fast trichrome (AFT) stain, and nested polymerase chain reaction (nPCR). Results:Microsporidium spp. was detected in 12 (8%) of samples using MTS. Compared with the other detection techniques the respective sensitivities and specificities of MZN stain was 100% and 98.57%; nPCR was 80% and 100%; and AFT was 85.71% and 97.87%. Conclusion: Using specific staining techniques as MZN and AFT for diagnosis of intestinal microsporidiosis in diarrheal stool samples are nearly as efficacious as PCR, but even better in some cases with the added advantage of being an inexpensive diagnostic method compared to PCR. Another benefit is the detection of other oocyst forming parasites such as Cryptosporidium, which makes staining techniques very suitable for developing countries