BACKGROUND: Chronic kidney disease (CKD) is global health concern and priority. It is the 12th leading cause of death worldwide. Protein Energy Wasting occurs in 20-25% of patients with chronic kidney disease and can lead to a high morbidity and mortality rate. We determined the prevalence of protein energy wasting and factors associated among patients with chronic kidney disease at Mulago National Referral Hospital, Kampala, Uganda. METHODS: We conducted a cross-sectional study recruiting 182 (89 non-CKD patients and 93 CKD patients) consecutively from the outpatient clinic and wards on New Mulago Hospital complex. We took anthropometric measurements including heights, weights, Triceps skin fold (TSF), Mid- Upper Arm circumference (MUAC), Body Mass Index (BMI) and Mid-arm muscle circumference (MAMC). Serum albumin levels and lipid profile levels were also obtained. Following consent of study participants, Data was collected using questionnaires and analyzed using STATA 14.1. Percentages, frequencies, means, medians, standard deviation and interquartile range were used to summarise data. Crude and adjusted binary logistic regression was performed to assess unadjusted and adjusted effect measures of protein energy wasting due to several factors. Stratification by CKD status was performed during the analysis to minimize confounding. RESULTS: The median age for CKD patients was 39 years compared to 27 years for non-CKD participants (p < 0.001). The prevalence of protein energy wasting (PEW) was 68.6% in this study with 47.3 and 21.3% among CKD and non-CKD participants respectively. Factors which were associated with PEW included CKD age between 18 and 24, being single, catholic religion, CKD stage 4, Hb < 11.5 g/dl and LDL > 160 mg/dl. CONCLUSION: Protein energy Wasting is prevalent among patients with chronic kidney disease and clinicians should routinely screen for it during patient care.