Progressive premature atherosclerosis and associated thromboembolic complications are the main causes of morbidity and mortality in patients with homocystinuria. However, thrombosis is rarely the predominant or presenting manifestation leading to the diagnosis of homocystinuria. We report on an otherwise asymptomatic teenage boy of normal intelligence who had a superior sagittal sinus thrombosis documented by CT and MRI scans. He presented with pneumothoraces, papilledema, and transient right hemiparesis. He subsequently developed empyema and necrotizing pneumonia as well as deep venous thromboses. The diagnosis of pyridoxine-unresponsive homocystinuria was made on the basis of clinical chemistry analyses, enzyme assay, and clinical trial. He has remained symptom-free under treatment with betaine and methionine restriction. We suggest that there exists a subset of patients with pyridoxine-unresponsive homocystinuria who are at risk for thromboembolism, but who may remain undiagnosed because of an otherwise mild clinical course.