Background: Ethiopia is found with a high HIV epidemic. HIV/AIDS and malnourishment worsen one another from different perspectives. In Sub-Saharan Africa including Ethiopia despite remarkable efforts to reduce the problems, HIV/AIDS and malnutrition has remained the main challenges of health systems. Objective: To assess malnutrition and identify factors associated with undernutrition among adult patients attending HIV follow-up service at Hiwot Fana Specialized University Hospital (HFSUH), Harar town, Eastern Ethiopia. Method: Institutional based cross-sectional study was conducted from November 1 to December 30, 2016, among five hundred two respondents. The sample was selected by a simple random sampling method from the pre-ART and ART sample frame. The data were collected using a structured questionnaire through face to face interviews. We used descriptive statistics to describe the prevalence of malnutrition and mean, frequencies, and proportion of the variables. Factors associated with undernutrition were assessed by a logistic regression model using STATA 14. Result: The