Cardiac catheterization is rarely performed in neonates in China. The medical records of 26 neonates who underwent cardiac catheterization in Shanghai Children's Medical Center from June 1994 to June 2004 were reviewed. These infants weighed 2 300 to 4 500 g (mean 3 400±500 g) . Postnatal age ranged from 5 to 28 days (mean 15.2± 8.7 days). Right heart ventricle angiography was performed in 24 cases, left heart ventricle angiography in 20 cases and pulmonary angiography in 6 cases. Balloon aortic septostomy(BAS) was performed in 10 cases. Twenty cases were diagnosed with complex cyanotic cardiovascular malformauions and 4 with acyanotic heart disease. The implantation of a temporary cardiac pacemaker was performed in 2 cases. All diagnostic and interventional procedures were successfully performed. The catheterization-related complications occurred in 15.3% of the 26 cases, but without mortality. In conclusion, cardiac catheterization is an accurate and safe method for diagnosing complex congenital heart diseases in neonates. Interventional catheterization is useful in the treatment of complex congenital heart malformations.