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Despite the increased emphasis on chronic non-communicable diseases, there are notable deficits about nutrition education in many medicine training programs particularly gastroenterology fellowship programs. In the present cross-sectional study, we examined the nutritional knowledge related to clinical nutrition among Iranian gastroenterology fellows. Thirty-six gastroenterology fellows currently enrolled in a gastroenterology fellowship program completed a questionnaire, including two sections. The first of which assessed the gastroenterology fellows experience about nutrition training, nutrition management of patients with gastrointestinal (GI) disorders and evaluating perceived nutrition education needs. The second section consisted of multiple choice questions that assessed nutritional knowledge. A total of 32 gastroenterology fellows completed the first section. The majority of gastroenterology fellows failed to partake in any nutrition education during their fellowship training particularly for inpatients despite the availability to participate in the nutrition training especially for the purpose of nutrition support. Mean correct response rates for the second section was 38%. The highest mean score was seen in nutrition assessment (48.1%), followed by scores of 40.5% in nutrition support, 37.0% nutrition in GI disease, and 25.0% in micro and macronutrients. Iranian gastroenterology fellows have serious deficits in their nutrition knowledge. This study paves the way for the development of an education program to improve nutritional knowledge of gastroenterology fellows.