This review examines the natural-colored, cross-sectional morphology of the foramen ovale (FO), ductus venosus (DV), right ventricle (RV), and pulmonary artery (PA) in fetal and neonatal rats. The ductus arteriosus (DA) and congenital heart disease are reviewed separately. The in situ cross-sectional morphology of fetal and neonatal rat hearts was studied by rapid whole-body freezing, slicing on a freezing microtome, and serially photographing the cross-sections every 0.5 mm with a stereoscopic microscope (Wild M400). The serial frontal sections of the fetal thorax and upper abdomen showed the fetal oxygenated blood route including the umbilical vein, DV, inferior vena cava, posterior right atrium, FO, and left atrium. Neonatal frontal sections of the same area revealed closure of the DV, FO, and DA, in addition to rapid enlargement of the peripheral pulmonary vessels. Neonatal closure of the FO was associated with remarkable growth of the atrial septum flap. The fetal atrial septum was short and thin at the FO, and the flap tip only just reached the rim of the FO. Neonatally, this atrial septum grew rapidly in length and thickness within two days, closing the FO.