HAND2 is an essential transcription factor for cardiac, pharyngeal arch, and limb development. Apoptosis in the HAND2-null embryo causes hypoplasia of the right ventricle and pharyngeal arches leading to lethality by embryonic day (E)10.0 from heart failure. In order to investigate the role of apoptosis in inducing the HAND2-null phenotype, we generated mouse embryos lacking both HAND2 and Apaf-1, a central downstream mediator of mitochondrial damage-induced apoptosis. In contrast to HAND2-/- embryos, HAND2-/-Apaf-1-/- embryos at E10.5-11.0 had well-developed pharyngeal arches, aortic arch arteries, and no signs of cardiac failure. TUNEL analysis through pharyngeal arches of HAND2-/-Apaf-1-/- embryos revealed decreased apoptosis and the embryos had clearly patent aortic arch arteries. However, ventricular hypoplasia and cell death were unchanged in these animals compared to HAND2-/- embryos, resulting in growth arrest at E11.0. Our study suggests that loss of HAND2 in the pharyngeal arch mesenchyme leads to apoptosis in an Apaf-1-dependent fashion and that, while loss of aortic arch integrity contributes to the early lethality, the ventricular defects are independent of arch development.