Aim: The aim of the study was to assess the prevalence of intestinal parasitic infections and associated factors among HIV positive and negative individuals visiting Kobo health center. Methods: A comparative cross-sectional study was conducted from April 2014 to July 2014. Each participant was interviewed for socio-demographic variables and stool specimen was collected from each participant and examined by direct wet mount and formol ether concentration technique. Data was analyzed using SPSS version 16.0 statistical programs. Results: A total of 100 individuals was involved during the study of which 50 of them were HIV positive and the rest 50 were HIV negative individuals. According to our study, intestinal parasites were found in 8 (16%) among the HIV-infected and 5 (10%) among the HIV-negative individuals. Of the study participants who were living with HIV/AIDS, the majority (12%) of them infected with intestinal parasites were females. Among the HIV positive individuals Ascaris lumbricoides 5 (62.5%), 2 (25%) Enterobius vermicularis were common, whereas Entamoeba histolytica 4 (80%) was the predominant parasite among the HIV negative individuals. Besides, multivariate logistic regression of HIV positive individuals also showed that sex, poor personal hygiene habits, and younger age were significantly associated with having intestinal parasites. Conclusion: Routine examination of stool samples for parasites would significantly benefit not only the HIV-infected patients, but also the uninfected individuals from contributing to reduce morbidity and improved quality of life.