Herein, we report a rare case of thyroid abscesses complicated by tracheal fistulae and multiple mediastinal abscesses in a patient with myelodysplastic syndrome. A 57-year-old female patient diagnosed with myelodysplastic syndrome three years earlier developed cough and fever and received antibiotic treatment in another clinic one week earlier; however, her condition had not improved, and she was referred to our hospital. Chest computed tomography (CT) showed multiple cysts and emphysema in bilateral upper lungs, nodules in the right upper and left lower lungs, and air in the thyroid isthmus and left lobe. Bronchoscopy revealed two tracheal fistulae and multiple protruding lesions, and contrast-enhanced CT revealed thyroid abscesses with air and multiple mediastinal abscesses around the trachea. The patient also had destructive thyroiditis. Although the causative agent could not be identified despite various culture tests, long-term antibiotic treatment led to improvement in her condition and all abscesses and fistulae disappeared.