We report a 4 year old boy in whom the clinical features of craniosynostosis and bilateral absent radii led to a diagnosis of Baller-Gerold syndrome. Additional congenital abnormalities included midface hypoplasia, atrial and ventricular septal defects, right hydronephrosis, partial sacral agenesis, and anterior ectopic anus. Evidence of portal venous hypertension was present from 8 months and a congenital portal venous malformation was discovered at 2 years. This is the first reported case of Baller-Gerold syndrome associated with a congenital portal venous malformation. We discuss the diagnostic confusion between this syndrome and other overlapping malformation syndromes and propose optimal evaluation strategies aimed at clarifying the nosology of these syndromes.