Most HIV clients die of AIDS related intestinal parasitic infections rather than due to the HIV infection itself. Therefore, this study was aimed at determining the prevalence of intestinal parasite and their associated factors among HIV/AIDS clients at the University of Gondar Hospital, Northwest Ethiopia. Institution based cross sectional study was conducted using systematic random sampling technique from March to May 2016. A semi-structured questionnaire was used to collect data. Stool samples were collected and processed using direct wet mount, formol-ether concentration and modified Ziehl-Neelson staining techniques. Besides, blood samples were collected for CD4+ count estimation. Both descriptive and logistic regression analyses were used in data analysis. P-values <0.05 were considered as statistically significant. A total of 223 participants were enrolled in this study, and the prevalence of intestinal parasitosis was found to be 29.1%. The most predominant intestinal parasite detected was cyst of Entamoeba histolytica (8.5%) followed by Ascaris lumbricoides (6.7%), Strongyloides sterocoralis (3.6%) and Cryptosporidium parvum (3.1%), whereas Schistosoma mansoni (0.9%) and Hymenolepis nana (0.9%) were the least detected. Absence of toilet (AOR= 19.4, CI: 6.46-58.3), improper hand washing before meal (AOR=11.23, 95% CI: 4.16-30.27 and CD4+ count < 200 cells/mm3 (AOR=33.31, 95% CI: 9.159-121.149) had significant association with prevalence of intestinal parasites. The study indicated that intestinal parasites are still a problem among HIV/AIDS patients in the study area. Thus, routine examination for intestinal parasites and interventions should be carried out for better management of clients.