This study was conducted to compare a conventional method of detecting the parasite in faecal samples and comparing it with molecular methods with reference to multiplex PCR to determine the difference in the level of sensitivity between them and to characterize the parasite detected to aid epidemiological studies. This cross–sectional study was carried out to detect Cryptosporidium parasites in HIV positive patients using Modified Ziehl Neelsen (MZN) Microscopy and Multiplex Polymerase Chain

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... action (Multiplex PCR). 49 fecal samples comprising 19 MZN –Positive samples and 30 MZN – negative diarrheic samples were analyzed using three (3) Polymerase Chain Reaction (PCR) approaches. A total of 15 samples that were positive by routine microscopy at University of Port Harcourt Teaching Hospital but negative by PCR and by microscopy in the laboratory were treated as false positives. Microscopy therefore exhibited 64% sensitivity and 72% specificity compared to PCR. Sensitivity, specificity, ability to genotype, ease of use, and adaptability to batch testing make PCR a useful tool for future diagnosis and studies on the molecular epidemiology of Cryptosporidium infections.