Objective To explore the clinical value of color Doppler ultrasoundcardiogram in the screening of congenital heart disease(CHD) in neonates. Methods 29568 neonates were examined by color Doppler ultrasoundcardiogram. Results 369 CHD patients were identified, the overall incidence of CHD was 12.48‰. The incidence in 2009 or 2010 were significantly higher than those in 2005 or 2004 ( all P ＜ 0. 05 ), the mean incidence of four years from 2007 to 2010 was significantly higher than that from 2003 to 2006( 13.78‰ vs 10.17‰,P ＜0. 01 ). Of 369 CHD cases,most of them were ventricular septal defect( occupied 48.24% ) ,next was atrial septal defect( occupied 44.17% ). Conclusion The incidence of CHD ascended rapidly from 2003 to 2010,and color Doppler ultrasoundcardiogram was an important method to diagnose CHD in newborns.