Alterations within the oral cavity can be the first sign of systemic diseases and may thus allow for an early diagnosis and treatment. In particular, being the oral cavity part of the gastrointestinal system, oral alterations can be an expression of a gastrointestinal disease. Dental enamel hypoplasia and aphthous ulcers have been found to be more common in children with coeliac disease compared with the general population and to regress after the patient is started on a gluten free-diet. A prompt recognition of systemic diseases through a careful examination of the oral cavity could allow the child to have appropriate investigations and to be treated in a timely fashion.