Congenital heart disease in patients with Down syndrome commonly has potential for early development of pulmonary hypertension. Moreover hypoventilation due to upper airway obstruction often causes severe pulmonary hypertension. We investigated how much hypoventilation had effect on pulmonary hypertension of cardiovascular anomalies. We reviewed the medical records of 65 Down syndrome patients who had cardiac catheterization between 1993 and 2008. Cardiac catheterization was performed under only intravenous sedation in 56 patients and under intubation in 9 patients. Study age was between 7 days and 11 months (median 5 months). They had cardiac malformations, left to right shunt such as ventricular septal defect, atrioventricular septal defect, patent ductus arteriosus and atrial septal defect. We defined mean pulmonary artery pressure 55mmHg or over as severe pulmonary hypertension, and arterial PCO2 46mmHg or over as hypoventilation. Contrary to our expectation there was no severe pulmonary hypertension in patients with intubation. In patients with only sedation severe pulmonary hypertension was significantly related to hypoventilation and high left atrial pressure by univariate analysis. Study age and cardiovascular malformation types showed no significant relationship to severe pulmonary hypertension. After multiple logistic regression model, severe pulmonary hypertension was independently associated with an odds ratio of 15.6(95%CI, 2.7-89.1:p=0.035) for hypoventilation, 5.3(95%CI, 1.1-25.4:p=0.002) for high pressure of left atrium(≧8mmHg). Under sedation pulmonary hypertension may be emphasized. Conversely under intubation, pulmonary hypertension may be underestimated. These results show that hypoventilation can easily bring about severe pulmonary hypertension in Down syndrome patients with left to right cardiovascular anomalies.