This paper provides recommendations for the nutritional management of children with chronic illnesses. Chronic diseases last for a long time and often substantially decrease the quality of life. They can increase the risk of stunting and affect the physical, mental and social life of children and adolescents and the whole family. Multidisciplinary team should treat this group of children in which the clinical dietitian plays an important role. Early identification of paediatric patients at risk, appropriate nutritional care and regular follow-up can have a significant impact on their health and the quality of life. This article presents some of the most common chronic diseases in the paediatric population for which nutritional management is of utmost importance. These include inflammatory bowel disease, food allergies, inborn errors of metabolism, autism spectrum disorders, cystic fibrosis, cancer and cerebral palsy.