Congenital diaphragmatic hernia (CDH) is often associated with other malformations. This study tests the hypothesis that the heart and great vessels, thymus, parathyroids, and thyroid might be abnormal in the rat model of CDH as a result of disturbed neural-crest development. Time-mated pregnant rats were fed either 100 mg 2-4-dichlorophenyl-p-nitrophenyl ether (nitrofen) or vehicle on gestational day 9.5. Diaphragm, lung, heart, and thymic malformations were sought after dissection and the parathyroids and thyroid were histologically investigated in term fetuses. Ten control fetuses had no malformations, whereas 22 of 32 nitrofen fetuses had CDH and 20 had cardiovascular defects like narrow pulmonary outflow tract (n = 7), aberrant right subclavian artery (n = 7), ventricular septal defect (n = 4), atrial septal defect (n = 4), tetralogy of Fallot (n = 2), double-outflow right ventricle (n = 2), right ductus arteriosus (n = 2), and others. The thymus was present but was significantly hypoplastic in all nitrofen fetuses and was ectopic or single-lobed in 28% of them while the parathyroid glands were unilaterally absent or ectopic in 50%. The thyroid was only minimally malformed or ectopic. In conclusion, malformations of structures derived from the pharyngeal arches are likely neural-crest related in rats exposed to nitrofen.