The Splotch mutant mouse shows defects in neural crest-derived cell populations. The septation of the truncus arteriosus and the development of the aortic arch-derived blood vessels was studied in homozygotes of the Splotch mutant allele Sp1H. It is shown that in homozygous mutant embryos, the septation of the truncus arteriosus does not proceed normally, resulting in persistent truncus arteriosus. The ostium of the persistent truncus arteriosus opens to the right ventricle. Frequently, variations of the aortic arch-derived blood vessels are observed. The development of the thymus, the parathyroid and the ultimobranchial bodies are also variably affected in mutants. These results provide indirect evidence, that cells contributing to the aortic arches and the septum of the truncus arteriosus in mice are derived from the neural crest. The Splotch mutant mouse is proposed to be an animal model for persistent truncus arteriosus. The implications of the vascular malformations for the midgestational death of this mutant are discussed.