Diarrhoea caused by Cryptosporidium is usually mild in immune competent individuals but severe in the young and those with underlying disease leading to compromised immunity. The conventional diagnosis of Cryptosporidium requires observation of the infective oocysts however, their tiny size yields indistinct results, thus limiting the effectiveness of the conventional diagnostic technique, modified Ziehl-Neelsen (ZN) differential staining. Consequent to the abovementioned limitation, ZN staining, sandwich antigen detection enzyme linked immunosorbent assay (sad-ELISA) and a direct polymerase chain reaction (PCR) assay techniques were evaluated for diagnostic efficacy. Stool samples were collected from 180 consenting adult patients attending outpatient and inpatient clinics at Victoria Hospital, Alice, Eastern Cape Province of South Africa. Subjects were stratified as; 35 HIV-positive and diarrhoeagenic, 125 HIV-negative diarrhoeagenic and 20 apparently healthy controls. Cryptosporidium incidence following diagnostic techniques were 13 (37.1%; ZN staining), 26 (74.3%; sad-ELISA) and 23 (65.7%; PCR), respectively, among HIV-positive diarrhoeagenic patients and 34 (27.2%; ZN staining), 96 (76.8%; sad-ELISA) and 89 (71.2%; PCR) among HIV-negative diarrhoeagenic patients. Sensitivity, specificity and predictive values of the diagnostic techniques’ efficiency were: sensitivity: 46.2% (HIV-positive) and 32.3% (HIV-negative) against the ZN technique and 96.9% against sad-ELISA and PCR, respectively, for both HIV-positive and -negative patients; specificity was 88.9% (HIV-positive) and 96.6% (HIV-negative) against the ZN technique. Lastly, the predictive values were 92.3% (HIV-positive) and 96.9% (HIV-negative), respectively, following ZN staining. The sad-ELISA technique proved more suitable for the determination of the presence of Cryptosporidium oocysts. The high incidence of Cryptosporidium in HIV-positive subjects as compared to the HIV-negative population accentuates the significance of cryptosporidiosis diagnosis in the treatment and management of HIV cases.