This study was designed to determine the prevalence of trabecular ventricular septal defect (t-VSD) in neonates and to evaluate the effects of its location, morphologic features, and size on its natural course during infancy. One thousand twenty-eight term newborn infants were examined by color Doppler flow imaging with orthogonal ultrasonographic views. Ten girls and 11 boys (2.0%) were found to have t-VSD. The natural course of the defect was examined in 42 consecutive cases, consisting of this group of 21 neonates and another group of 21 neonates with t-VSD. The morphologic features of the defect within the trabecular septum were classified as one or two defects (36 cases) and as a mesh-like defect (six cases). Reduction in size began from the right ventricular side or from within the trabecular septum. Spontaneous closure occurred most commonly during the first 6 months of life and was observed in 32 cases (76%) by 12 months of age: the frequency of closure was not related to the morphologic features and the initial size of the defect, but apical defects tended to have higher persistent patency than did defects in other locations (p less than 0.05). We conclude that the frequency of t-VSD in neonates and the frequency of spontaneous closure during early infancy are higher than previously believed. This information is important for predicting the natural course of t-VSD and deciding on its proper management.