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The 7-month-old girl was left in a nursery until following morning. About 3 h after being given milk, she was found dead in a right lateral supine position. There was no external evidence of injury to suggest a maltreatment. Hemorrhages were present in the accessory respiratory muscles, but the most notable findings were masses on either side of the trachea and immediately inferior to the thyroid gland. Both of masses were in continuity with the intrathoracic thymus. Histopathologically, the masses showed normal thymic structure and collagen fibers on the left side of the trachea showed metachromasia on Masson’s staining. There were no remarkable findings in organs except for congestion. The cause of death was determined to be mechanical asphyxia due to tracheal compression by the cervical ectopic thymus. Hemorrhage in the accessory respiratory muscle was considered to be caused by effortful breathing during the process of asphyxia. The metachromasia of Masson's stain on the trachea may be due to the same mechanism as a “compression mark reaction”, and may be useful in proving compression by the ectopic thymus. We consider that chronic compression of the trachea led to the tracheomalacia, which enabled the final lethal compression when lying in a right lateral supine position. An ectopic thymus is caused by a failure of descent of the embryonic thymic tissue into the thoracic cavity at the appropriate developmental stage and is generally asymptomatic. However, the cervical ectopic thymus should be considered in the diagnosis of a cause of sudden infant death.