Echocardiography and magnetic resonance imaging revealed biventricular non-compaction cardiomyopathy with ventricular (VSD) and atrial (ASD) septal defects in an unconscious, 23-year-old hypoxemic man. Doppler echocardiography showed a left-to-right shunt across the VSD and a right-to-left shunt across the ASD. Cardiac catheterization revealed elevated right atrial pressure, although pulmonary pressure was normal. We considered that the atrial right-to-left shunt had induced the hypoxemia, which was related mainly to right ventricular dysfunction in this biventricular non-compaction cardiomyopathy, but it was not related to pulmonary hypertension.