Cryptosporidium parvum is endemic to South Africa. In order to provide direction for prevention strategies, information on the dominant genotype involved in human infections is required. A combination of diethyl ether extraction, sodium chloride flotation and immuno-magnetic separation (IMS) was used for maximum recovery of oocysts from faecal samples. In order to improve the sensitivity of PCR-RFLP analysis of the Cryptosporidium oocyst wall protein (COWP) gene, a nested PCR was developed. RFLP analysis was done on a 553 bp segment obtained from the final nested PCR reaction to distinguish between C. parvum genotype 1 (human exclusive type) and genotype 2 (broad host range). Overall, genotype 2 was detected in 10 samples, whereas genotype 1 was detected in the remaining 40 samples. The high incidence of genotype 1 parasites (80%) implies that direct and indirect human transmission plays a dominant role in the epidemiology of the disease caused by this parasite in the study area.