Background: Cryptosporidium oocysts detection methods include alternate bright-field stains and negative stains. These methods show high sensitivities but it may leave some oocysts unstained.                             Objective: Evaluation of the direct fluorescence antibody (DFA) and coproantigens by ELISA versus modified Ziehl–Neelsen (MZN) stained smears in detection of Cryptosporidium.  Material and Methods: Eighty two immunocompromised patients having acute/ chronic diarrhea, were selected from the attendants of the pediatrics, oncology and nephrology clinics in Al-Azhar University Hospitals, during the period from August 2013 to May 2014. All cases were subjected to history taking and clinical examination, laboratoryexaminationof their fecal smears by microscopic examination of MZN stained smears, detection of coproantigens by ELISA and DFA for diagnosis of Cryptosporidium. Results: Fifteen (18.29%) of the individuals were positive for Cryptosporidium infection using modified Ziehl–Neelsen stain, and 17 (20.73%) were positive by direct fluorescent antibody, while ELISA detect crypto-coproantigen in 18 (21.95%). Statistically, there were highly significant relations between ELISA, DFA, and MZN. The sensitivity, specificity, and positive and negative predictive values of DFA test were 100, 97, 88.2 and 100 %, respectively, and for ELISA test were 100, 95.5, 83.3 and 100%, respectively, compared with MZN method as the gold standard test for detection of the Cryptosporidium .     Conclusion: Modified Ziehl-Neelsen staining remained the gold standard for the detection of Cryptosporidium spp., but it may leave some oocysts unstained. So, the immunofluorescence assays were the methods of choice for greatest sensitivity and specificity especially when oocyst numbers in stool specimens were low.