Objective To research the visualization of congenital heart disease by three-dimensional echocardiographic(3DE) virtual endoscopy(VE) system. Methods Datasets.from 10 healthy children and 22 patients with congenital heart disease were collected (10 patients with atrial septal defects, 6 patients with ventricular septal defects and 6 patients with tetralogy of Fallot). 3DE heart models were reconstructed by virtual reality computing techniques and visualization in scientific computing techniques. The VE system was programmed under the C++ 6.0 language condition,the visualization toolkit (VTK) platform was employed to carry out the graphics and visualization utilities. The virtual eye can move along the navigation paths in the heart by manual camera movements. Results The VE can provide special information in aspects of intracardiac anatomy, The visible heart models show precisely complex anatomy structure and spatial relationships. 3DE intracardiac endoscopic imaging can thus be visualized and navigated successfully by the VE system. Conclusions 3DE VE is a new system for the visualization of congenital heart disease.