Histamine intolerance is defined as disequilibrium of accumulated histamine and the capacity for histamine degradation. This clinical term addresses a non-immunologically mediated pathology when histamine ingested with food is not particularly high, but its degradation is decreased. Clinical picture of histamine intolerance in children is similar to that observed in adults apart from male predominance found in paediatric patients. Both in children and adults, histamine-free diet seems to be the treatment of choice. Diamine oxidase supplementation offers another treatment option. There is no symptom and\or test pathognomonic for histamine intolerance. Nevertheless, manifestations of chronic gastrointestinal symptoms, measurement of diamine oxidase deficits, positive results of histamine provocation tests and improvement of symptoms with histamine-free diet greatly increase the probability of histamine intolerance diagnosis. These factors have been included in the proposed in this paper diagnostic algorithm for histamine intolerance. In children histamine intolerance probably co-occur with allergies and bowel diseases, which creates an additional diagnostic challenge. As the evidence for children is weak, further research is needed the establish epidemiology, validate diagnostic algorithms and establish possible treatment options regarding histamine intolerance.