Aim: Although cryptosporidiosis is said to be rare among adult HIV patients in certain parts of Nigeria, there are no documented studies on the occurrence of this parasite among HIV patients in Southwestern Nigeria. Methods: We conducted a cross sectional study involving 150 patients (100 HIV infected and 50 HIV negative) with diarrhoea from two tertiary and one secondary health institutions in Southwestern Nigeria. Concentrated stool sample from each patient was screened for cryptosporidium oocysts with the modified cold Ziehl Neelsen method while direct sample was screened for other enteric parasites. Results: The overall parasite prevalence rate in the diarrhoea patients is 79.3% (119/150) with Cryptosporidium parvum 52.7%, Ascaris lumbricoides 11.3%, Hookworm 3.3%, Trichuris trichura 2% and Entamoeba histolytica 10%. The parasite prevalence rate in HIV infected patients is 97% while in HIV-negative patients, the rate is 44%. The rate is significantly higher among HIVinfected patients with diarrhoea than among HIV-negative patients with diarrhoea (OR=41.152, 95%CI=11.467-147.68, P<0.0001). However this difference is attributed to Cryptosporidium which was found exclusively among HIV-infected patients. When Cryptosporidium prevalence was excluded from analysis, the parasite prevalence rates between the two groups was not significantly different (X2=0.8002, df=3, P=0.8494). Conclusion: Contrary to a previous report of apparent rarity of cryptosporidium infections in certain parts of Nigeria, this study revealed a high prevalence of this parasitosis among HIV infected patients in Southwestern Nigeria.