Jugular vein thrombosis (JVT) is usually secondary to central venous catheterisation, distant malignancy, hypercoagulable state or ovarian hyperstimulation syndrome. Spontaneous internal JVT is an extremely rare entity. A 61-year-old man presented with swelling of the right side of his face. An ultrasonographic scan showed thrombosis of the right jugular vein. Clinical tests, including oncomarkers, X-ray, CT scan and abdominal ultrasonography, searching for malignancy, were negative. The patient was heparinized immediately using LMWH and then underwent warfarin anticoagulation therapy for 6 months. One year later the patient was in good clinical condition with no malignancy diagnosed. Aetiology and the treatment of spontaneous JVT are discussed.