On the basis of our recent embryologic work concerning the separation process of the outflow tract, together with our study of the morphology of specimens from the Leiden Collection of malformed hearts, we have reconsidered, in conjunction with the pertinent literature, the morphogenesis of common arterial trunk and tetralogy of Fallot. The constant characteristics of common arterial trunk, namely a common trunk, a common arterial orifice and a ventricular septal defect, can be explained simply by absence of the aorto-pulmonary septum, or its complete failure to contribute to the process of separation. The nature of the variable morphologic features, however, is not always clear. Presence of such variation is not contradictory to the explanation of the main characteristics in this malformation. Tetralogy of Fallot, in contrast, can be considered to result from anterior displacement of the columns of the aorto-pulmonary septum relative to the outlet segment and its proximal boundary, the primary fold. Our findings, and suggestions, diverge considerably from conventional theories concerning the morphogenesis of these malformations.