Children with heterotaxy syndrome frequently have complex cardiac and noncardiac malformations requiring detailed diagnostic evaluation for management planning. Direct delineation of these structures by electron beam computed tomography (EBCT) is validated as a means of diagnosis. From July 1995 to March 1997, 32 patients (16 girls, 16 boys) with clinically impressed heterotaxy syndrome were enrolled in this study. After evaluation by echocardiography, EBCT studies were performed. Interpretation of cardiac anomalies was performed by sequential analysis based on these cross-sectional images. The diagnoses were subsequently confirmed by angiocardiography and surgical findings. Twenty-eight patients had bilateral trifurcated bronchi, and most of these (24 of 28) did not have a spleen. Four patients had bilateral bifurcated bronchi, 2 patients had polysplenia, and the other 2 patients had a lobulated single spleen. We found that laterality could be identified by EBCT in all patients. Comparison of diagnostic yield between echocardiography, catheterization, and EBCT showed that EBCT is superior to echocardiography and catheterization in demonstration of pulmonary venous anatomy and presence of a very small rudimentary ventricle. In addition, associated visceral, bronchopulmonary, mediastinal, and intracardiac anomalies could all be clearly delineated by EBCT at the same time. Thus, EBCT is a promising complementary modality for an overall understanding of heterotaxy syndrome.