Background: Previous studies from high altitudes have reported significantly higher prevalence of congenital heart disease (CHD), consisting almost solely of simple CHD. Little is known about the occurrence of complex CHD. Neonates with complex CHD are likely admitted to NICU. We examined the prevalence and spectrum of complex CHD in NICU in order to depict a truer picture of CHD at high altitude. Methods: We reviewed charts of 4,214 neonates admitted to NICU in Qinghai province (average altitude 3,000 m). Echocardiography was performed in 1,943 babies when CHD was suspected based on clinical examinations. Results: CHD was diagnosed in 1,093 (56.3% of echoed babies). Mild CHD in 96.8% (1058 babies). Moderate CHD in 0.8% (9) included 1 (0.1%) large secundum atrial septal defect, 3 (0.3%) moderate pulmonary stenosis, 2 (0.2%) aortic stenosis and 3 (0.3%) partial anomalous pulmonary venous connection. Severe CHD in 2.4% (26) included 6 (05%) complete atrioventricular septal defect, 5 (0.5%) complete transposition of the great arteries, 5 (0.5%) hypoplastic right heart, 3 (03%) hypoplastic left heart, 3 (03%) double outlet right ventricle, 3 (0.3%) tetralogy of Fallot, 2 (0.2%) tnuicus arteriosus, 2 (0.2%) total anomalous pulmonary venous connection, 2 (0.2%) severe aortic stenosis, 2 (0.2%) interrupted aortic arch and 2 (0.2%) severe pulmonary stenosis and 1 (0.1%) single-ventricle abnormality. At two-years follow-up in 737 (67.4%) patients, 18 (90%) with severe CHD and 38 (5.3%) with mild and moderate CHD died, and 15 underwent cardiac surgery with 1 early death. Conclusions: At high altitude, a wide spectrum of CHD exists, with many heretofore unreported complex CHD. There is urgent need for routine echocardiography and early interventions in newborns particularly in NICU.