Background Primary thyroid leiomyosarcoma (LMS) is a very rare tumour with less than 40 published cases yet. Direct metastatic extension into the great cervical veins and caval veins is extremely uncommon. Extension to the right heart has not yet been reported. Case summary A 62-year-old man was admitted for sudden onset of left neck pain and dyspnoea. CT and ultrasonography found an extensive mass of the left great cervical veins, superior vena cava, and a nodule in the left thyroid lobe. Transesophageal echocardiography visualized large protrusion of this mass into the right atrium. Cytology of a thyroid nodule diagnosed a benign hyperplastic nodule. The mass was considered to be likely an extensive thrombus. The patient was started on anticoagulant therapy. The next course was complicated by pulmonary embolism and later by enterorrhagia. Despite clinical stabilization, the patient died suddenly. Autopsy finding differed from the clinical conclusion. Microscopic investigation revealed that the mass seen in the cervical veins down to the right atrium was a spindle cell tumour with a primary site in the left thyroid lobe. Immunohistochemistry was consistent with the final diagnosis of primary thyroid LMS. Discussion Differential diagnosis of the masses of great cervical veins and right atrium can be challenging. Pure venous thrombus and tumour thrombus must be distinguished. Thyroid LMS should also be considered in patients with masses in the right atrium and thyroid nodules.