Background: Inflammation plays an important role in pathogenesis of cystic fibrosis, and diet is considered as an effective factor in controlling inflammation. Low glycemic index diet seems to be effective for improving glycemic control and reducing the inflammation and lipid profile. Hence, this study was planned to compare the effects of a low glycemic index/high fat, high calorie diet with the high fat, high calorie diet on glycemic status, lipid profile, and inflammatory markers in patients with cystic fibrosis. Methods: A total of 60 children and adolescence with cystic fibrosis will be randomized to receive a high fat, high calorie diet (n=30) or low glycemic index/high fat, high calorie diet (n=30) with similar calorie and macronutrients composition, for three months. Patients in high fat, high calorie diet arm will be able to use all sources of carbohydrates with different glycaemic indices; while those in another arm will be received their carbohydrate from low glycemic index sources. Before and after the intervention, serum levels of lipid profile (triglyceride, total cholesterol, HDL cholesterol, LDL cholesterol), insulin, glucose, HbA1c, the homeostasis model assessment-estimated insulin resistance index, and some inflammatory markers (IL-6, IL-10, IL-17A, and IFNγ) will be measured. Discussion: To our knowledge, this study will be the first to examine the effects of a low glycemic index/high fat, high calorie diet compared to the high fat, high calorie diet in cystic fibrosis patients. The findings of this study might provide evidence to improve the nutritional status and immune system as well as to prevent the disease complications in these patients.