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Exclusion diets are an increasingly used tool in the paediatric population to manage a broad range of gastrointestinal (GI) conditions like irritable bowel syndrome, lactose intolerance, coeliac disease, eosinophilic oesophagitis, gastro-oesophageal reflux disease, inflammatory bowel disease, cow’s milk protein allergy or food protein induced enterocolitis syndrome. While the evidence indisputably supports their effectiveness in some of these pathologies, in others it is extremely limited. An important aspect that needs to be considered when these diets are implemented is the potential risks associated, especially in the absence of clinical and dietetical support. These risks involve not only the expected nutritional deficiencies and possible negative effects on growth and development, but also important negative psychological outcomes (eg, food aversion, eating disorders) and a reduced quality of life. The reintroduction of foods, if possible, is essential to avoid possible complications associated with long-term restrictions. Overall, while the exclusion diets can be used as an effective treatment strategy in certain GI conditions, this use must be evidence-based, time-limited if possible and guided by specialist healthcare professionals. This review summarises the current evidence regarding the indications, benefits and risks of exclusion diets in children and provides evidence-based guidance for their safe and effective implementation.