The developing heart and great vessels undergo drastic morphogenetic changes during the embryonic period. To analyze the normal and abnormal development of these organs, it is essential to visualize their structures in three and four dimensions, including the changes occurring with time. We have reconstructed the luminal structure of the hearts and great vessels of staged human embryos from serial histological sections to demonstrate their sequential morphological changes in three dimensions. The detailed structures of the embryonic heart and major arteries in normal and holoprosencephalic (HPE) human embryos could be reconstructed and visualized, and anatomical structures were analyzed using 3D images. By 3D analysis, cardiac anomalies such as double-outlet right ventricle and malrotation of the heart tube were identified in HPE embryos, which were not easily diagnosed by histological observation. Reconstruction and analysis of 3D images are useful for the study of anatomical structures of developing embryos and for identifying their abnormalities.