Tracheoinnominate artery fistula is a well-known complication that arises on using a cannula. Therefore, routine examination of the anatomical relationship of the innominate artery and trachea should be carried out. We evaluated the usefulness of magnetic resonance imaging in 5 patients with severe motor and intellectual disabilities (SMID) using a combination of true-fast imaging of steady-state precession (true-FISP) sequences and two-dimensional prospective acquisition correction (2D-PACE). For all patients, the trachea and the innominate artery were identified without sedation and contrast media. In one patient, the innominate artery was observed to be pressing on the trachea. In three patients, the trachea and innominate artery were brought very close each other, and in the other patient the anatomical relationship of the trachea and surrounding structure was delineated before tracheotomy. The validity of true-FISP sequences combined with the respiratory-gated technique was confirmed useful for the patients who are difficult to lie quietly and to hold their breath voluntarily.