We show that patients with deletions harboring FOXF1 and the neighboring FOXC2 (MIM 602402) and FOXL1 (MIM 603252) genes at 16q24.1 have not only ACD/MPV, as expected, but also distinct malformations comprising congenital heart defect, in particular hypoplastic left heart syndrome, and gastrointestinal atresias, including esophageal atresia, as well as urinary tract malformations and other malformations. This evidence concerns the gene FOXF1 and hypoplastic left heart syndrome.