Cryptosporidium spp. is considered one of the most common diarrhea-causing protozoa. This cross-sectional study was designed for molecular detection of Cryptosporidium spp., comparing results with microscopy using Acid Fast (AF) staining, and to determine predominance of cryptosporidiosis according to patients' age and gender. Methodology: Stool samples were collected from 150 diarrheic patients attending outpatient clinics of Kasr Al-Ainy School of Medicine, Cairo University. Samples were examined microscopically by direct wet mount before and after sample concentration, and then subjected to copro-PCR assays. The results showed that out of 150 samples subjected to nPCR, only 9 (6%) samples were
positive for Cryptosporidium spp. and of those, 2 (1.3%) were positive by microscopy using AF stain. Microscopy showed high specificity but lower sensitivity (22%) compared to nPCR. Six of the 9 molecularly positive cases (66.7%) were children under 9 years and predominantly females with statistical significance.