Obstruction and thrombosis of major systemic veins can occur due to indwelling central venous catheters. If obstruction of the innominate vein or superior vena cava occurs, lymphatic drainage can be impaired due to an increase in pressure in the thoracic duct and lymphatics. We describe a case where superior vena cava syndrome, chylopericardium and chylothorax occurred in a 16-year-old girl due to an indwelling central venous catheter. This was successfully treated with removal of the line, anticoagulation and angioplasty of the innominate vein and superior vena cava.