Most Kawasaki patients recover fully from the disease, with no complications later in life. However, approximately 20% will experience cardiac problems caused by the persistence and/or progressive change of weak areas or swellings in the coronary arteries. Also, the coronary artery walls tend to be somewhat thicker and less flexible than normal after the disease, either through calcification (hardening of artery walls) or the early development of atherosclerosis (deposition of fatty materials on the artery walls).

Normally, aneurysms resulting from Kawasaki Disease will decrease in size as the patient ages. Smaller lesions are more likely to heal completely than larger ones, and the younger a patient was at the time of outbreak, the more likely it is for the aneurysms to disappear.

Those aneurysms that persist in the older patient have a tendency to become narrow (stenotic) or blocked (occluded) over time. Larger aneurysms may contribute to the sluggish flow of blood through the artery, which may promote the formation of blood clots (thromboses). Any narrowing or blockage of the coronary arteries can lead to the disruption of the oxygen supply to the heart muscle, resulting in a heart attack.

Because of these risks, Kawasaki patients are now advised to have their condition monitored through life, with counseling by a physician and a check-up once every five years, in most cases.  Older children with a history of Pharmaceutical therapy may be necessary for patients with persistent aneurysms. The development of coronary abnormalities may be accelerated by smoking, hypertension (high blood pressure), and hyperlipidemia (high cholesterol and other fatty substances in the blood stream).