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The application of a computer-assisted, three-dimensional reconstruction procedure for serial sections to embryonic rat hearts during the period of cardiac looping and compartmentalization is described. The procedure relies on immunohistochemical staining for the introduction of selective contrast and on episcopic and diascopic images of each of the sections for alignment and correction of compression due to sectioning. Episcopic (reference) images are taken from the embedding block just before the cutting of a slice and are still aligned and undeformed. Diascopic images are taken from the sections after immunohistochemical processing and, hence, contain selective contrast but are deformed and no longer aligned. The three-dimensional images are visualized as shaded voxel models. This approach allowed the unequivocal delineation of the developing myocardium and the inspection of its changing architecture both from the outside and from within. Furthermore, it allowed a quantification of myocardial volume. Because standardized and hence comparable views of three different stages were generated, changes in the shape of the cardiac loop, the atria, and the ventricles as well as changes in the position of the atrioventricular canal and interventricular foramen could be accurately described. Characteristic changes in the position of both the right ventricle and the atrioventricular canal that are essential for the formation of a correctly functioning four-chambered heart could be observed. These changes in shape occur while the myocardial size increases dramatically.