An infant girl, born small for gestational age, with abnormal single creases on the fifth digits, subsequent severe developmental delay, hypertelorism, bilateral equinovalgus deformities, grade IV genitourinary reflux and mild right hydronephrosis, was found to have an inverted duplication of the short arm of chromosome 16 [46,XX; inv dup (16) (p 13.3-->p 11.2]. The cardiac anomalies included a large perimembranous ventricular septal defect (VSD) and a moderate-sized atrial septal defect (ASD). Cardiac catheterization at 6 months of age revealed systemic level pulmonary artery pressure, bilateral pulmonary venous desaturation, and in room air a pulmonary/systemic blood flow ratio (Qp/Qs) of 0.8:1.0, which did not change significantly with administration of oxygen and nitric oxide. To our knowledge, this is the first description of early nonreactive pulmonary vascular disease in a patient with duplication 16p and a large VSD.