Anaemia is a common problem encountered by paediatricians and general practitioners in the paediatric population. If left untreated, it can lead to serious health consequences, slower development and cognitive impairment. Therefore, it is extremely important to identify its cause and implement appropriate treatment. Since iron deficiency is the most common cause of anaemia, oral iron supplementation at appropriate doses should be used as a first step. However, anaemia may be secondary and often the only symptom of pathological processes in the body. It very often accompanies gastrointestinal diseases, which cause impaired absorption of hematopoietic elements, blood loss through the gastrointestinal tract and dysregulation of iron metabolism accompanying chronic diseases. Therefore, anaemia unresponsive to oral iron treatment should prompt diagnosis for gastrointestinal diseases most common in the paediatric population. Specialised investigations should target the suspected clinical entity, enabling its diagnosis. A correct diagnosis allows for optimal treatment of the underlying disease and, as a result, resolution of the pathology triggering anaemia. However, it takes a long time to regain normal intestinal mucosal function, therefore it is often necessary to additionally include intravenous iron infusions and, in selected cases, packed red blood cell transfusions to rapidly normalise red cell system parameters.