An eight-month-old girl with hypoplastic left heart syndrome, who underwent a modified Norwood operation at the age of two days, and a Hemifontan operation at five months of age, had severely impaired ventricular function and new electrocardiographic changes. Coronary angiography demonstrated a small adherent thrombus in the non-coronary sinus of Valsalva of the native aortic root, which may be the cause of unexplained ventricular dysfunction.