Cryptosporidium is one of the most common human parasitic protozoa that is responsible for many waterborne outbreaks in several industrialized countries. Infection is usually self-limited in immunocompetent population, but it can be severe and life-threatening among immunocompromized individuals. The present work aimed to assess the real-time PCR based method and coproantigen ELISA in diagnosis of cryptosporidiosis and compare be-tween both methods with conventional microscopy. The present study was carried out on 219 cases, all of them were subjected to full history, stool examination (direct wet mount, Lugo’s iodine and formol ether sedimentation technique), detection of Cryptosporidium oocysts by using modified Ziehl-Neelsen stain (MZN), detection of cryptosporidial coproantigens using ELISA technique, molecular detection of cryptosporidial infection using Real- time PCR. It was found that Cryptosporidium oocysts have been detected in formed stool (53.3%) more than diarrheic stool (32.1%) and semi formed stool (14.6%). Sensitivity, specificity, positive predictive value and negative predictive value for ELISA in detection of cryptosporidial copro- antigens were 93.4%, 86.7%, 97% and 74.3% respectively in comparison to MZN staining. Sensitivity, specificity, positive predictive value and negative predictive value for PCR in detection of cryptosporidial infection were (19%), (100%), (100%), (21.3%) respectively, in comparison to MZN staining. Comparison of positive results detected by different techniques revealed that MZN stain was more sensitive than ELISA and PCR, ELISA was more sensitive than PCR but PCR was more specific than ELISA. In conclusion, immunological diagnosis of cryptosporidiosis by ELI-SA test is simple and rapid method, it’s also sensitive and specific but less than MZN staining and molecular detection of cryptosporidial infection using Real-time PCR is specific technique but it’s less sensitive than MZN staining and ELISA test. Real-time PCR is expensive, laborious and need strict aseptic conditions. Stool examination using MZN staining is still the routine method in diagnosis of Cryptosporidium infection as it’s sensitive, cheap, simple to perform and available even in poor health care unites.