Background Malnutrition especially undernutrition is the main problem that is seen over people living with HIV/AIDS and can occur at any age. Multiple factors contributed to undernutrition of HIV/ AIDS patients and it need immediate identification and prompt action. The objective of this study was to assess the nutritional status of patients and identify factors associated with undernutrition among HIV/AIDS patients on follow-up care in Jimma medical center, Southwest Ethiopia. Methods A cross-sectional study design was conducted from March-April 2016. Data were collected retrospectively from clinical records of HIV/AIDS patients enrolled for follow up care in ART clinic from June 2010 to January 2016. Bivariate and multivariate logistic regression analysis were performed to identify independent predictor of undernutrition. Results Data of 1062 patients were included in the study. The prevalence of undernutrition (BMI<18.5 kg/m 2) and overweight or obesity were 34% and 9%, respectively. Out of undernourished patients, severely malnourished patients (BMI<16 kg/m 2) accounted of 9%. Undernutrition was more likely among widowed patients (AOR = 1.7, 95% CI, 1.03-2.79), patients with no access to water supply (AOR = 1.69, 95% CI, 1.16-2.47) and patients in the WHO clinical stage of three (AOR = 2.0, 95% CI, 1.33-2.97) and four (AOR = 3.0, 95% CI, 1.74-5.07). Moreover, the odds of undernutrition was more likely among patients with CD4 cell count of <200 cells/mm 3 (AOR = 2.0, 95% CI, 1.38-2.47) and patients with a functional status of bedridden (