We report a 4-week-old boy with acute respiratory distress, due to massive haemorrhages in multiple thymic cysts. A right hemithymectomy was performed because of mechanical obstruction of the trachea by the cysts. The origin of the multilocular thymic cysts remained unclear. Most likely, these haemorrhages were caused by vitamin K deficiency, although the infant received vitamin K prophylaxis. In addition, he developed transient cholestasis, but the aetiology remained unclear. It is postulated that massive haemorrhages in thymic cysts produce large amounts of bilirubin, causing sludging of bile excretions in the liver. Four weeks after the operation, all laboratory findings were normal and 6 months after the operation the boy is still healthy. Conclusion This case report shows that respiratory distress in an infant can be caused by multiple haemorrhages in multilocular thymic cysts.