Heart failure is a major cause of mortality and morbidity in children. Heart transplantation can significantly improve the prognosis of patients with severe heart failure, but access is limited by a shortage of transplants. Long-term mechanical circulatory support is a major advance in the management of heart failure and can provide haemodynamic support while awaiting myocardial recovery or heart transplantation. The Berlin Heart (BH) EXCOR is the only long-term support system available for children. Despite technical and medical advances in circulatory support, infection is a common complication and a major cause of morbidity and mortality in patients on BH. There are few studies on the management of infection with mechanical support. Current ISHLT (International Society for Heart and Lung Transplantation) recommendations are based on expert opinion and observational studies. Some experts recommend anti-infective therapy until transplantation for specific support infections or for support-associated infections with persistent bacteraemia.