BackgroundIntestinal parasites are a major concern in most developing countries where HIV/AIDS case are concentrate and almost 80% of AIDS patients die of AIDS-related infections. In the absence of ART, HIV/AIDS patients in developing countries unfortunately continue to suffer from the consequences of opportunistic parasites. But this prevalence has dramatically decreased in countries where antiretroviral agents are widely available. Therefore, the aim of this study was to assess the prevalence of intestinal parasite and risk factor among pre- ART and on ART adult HIV/ AIDS patients attending ART clinic in Dessie hospital.MethodsA comparative cross-sectional study was conducted among pre-ART and on ART adult HIV/AIDS patients of Dessie Hospital. A total of 272 (136 from each group) study subjects were selected by using systematic random sampling. Stool sample was collected and processed using direct wet mount, formol-ether concentration technique and modified Ziehl-Neelson staining techniques. A structured questionnaire was used to collect data on Sociodemographic & associated risk factors. Data was entered and analyzed by using SPSS 16 software and logistic regressions were applied to assess any association between explanatory factors and outcome variables.ResultsThe overall prevalence of IP in pre-ART and on-ART was 39% and 17.6%, respectively with significant decrease of intestinal parasite in the ART era (p < 0.001). All Cryptosporidium spps infections were found in the pre-ART patients and significantly associated for lower CD4 <200cells/mm3. Absence of toilet (AOR = 7.57; 95% CI = 1.3,44.22), source of water (AOR = 6.03; 95% CI = 1.14,31.98), living condition (AOR = 13.29, 95% CI = 5.14, 34.35); WHO stage (AOR = 6.06; 95% CI = 2.49,14.74) and ART status (AOR = 7.55; 95% CI = 3.24,17.59) have significant association with prevalence of intestinal parasite.ConclusionThe overall prevalence of IP was differ by ART status and opportunistic parasite like cryptosporidium spps were found in low CD4 counts in ART naive patients. This study identified some environmental and some clinical finding as determinant factor for IP infections. Therefore, public health measures and adherence to ART should be strengthened to improve the quality of life of these patients.