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Background Cryptosporidium spp and I. belli are intestinal opportunistic infections associated with HIV/AIDS. A decline in the incidence of these opportunistic infections due to HAART was reported. We aim to investigate these parasites among HAART naïve and experienced HIV patients in south Ethiopia. Methods A cross sectional study was carried out among 268 HIV- positive patients between January and September, 2007. Interview with questionnaires and document reviews were used to collect data. Stool samples were obtained from each patient and parasites were examined by direct, formol-ether and modified Ziehl-Neelsen stain for Cryptosporidium spp and I. belli. Univariate and multivariate analysis were carried out. Level of significance was set at p-value of 0.05. Results A total of 268 patients participated in the study. The mean age was 34.0 (±1 SD of 8.34) years. Females constituted 53.4% (143) of the study participants. Half of the study participants were on HAART; majorities (85.8%) of such patients were within the first year of treatment. The prevalence of Cryptosporidium spp was 34.3% (92/268) and I. belli was 1.5% (4/268). Dual infection was detected in two patients (0.75%). The crude analysis revealed significant reduction in the odds of Cryptosporidium spp infection among patients who have started HAART (crude OR = 0.59, 95% CI 0.35, 0.98). The adjusted analysis remained in the same direction but has lost significance (Adj OR 0.65, 95%CI 0.35, 1.24). No differences in the risk of developing infection with Cryptosporidium spp were observed between groups based on most recent CD4 counts, sex, duration on HAART and age (p > 0.05 for all variables). Patients with Cryptosporidium spp were more likely to report vomiting [Adj OR 2.34 (95% CI 1.22, 5.41)], weight loss [Adj OR 2.10 (95% CI 1.15, 3.81)] and chronic diarrhea [Adj OR 3.35 (95%CI 1.05, 10.63)]. Conclusion There is high burden of infection with Cryptosporidium spp among HIV infected individuals in southern Ethiopia but that of I. belli is low. We recommend considering infection with Cryptosporidium spp in HIV infected people with chronic diarrhea, weight loss and vomiting for HAART naïve patients and/or for patients who are within the first year of starting HAART. [ABSTRACT FROM AUTHOR]