We report on visceral anomalies found in 136 patients with Apert syndrome. Autopsies were only performed on 12 of these cases. Thus, the percentage of anomalies found in our patients should be considered a minimum estimate because of the possibility of clinically silent visceral anomalies, minor internal anomalies, and anatomic variations. Cardiovascular and genitourinary anomalies were found most commonly, occurring in 10% and 9.6%, respectively. As expected, complex and multiple cardiac anomalies were frequently associated with early death. Among genitourinary anomalies, hydronephrosis (3%) and cryptorchidism (4.5%, n = 66 males) occurred most commonly. In contrast, anomalies of the respiratory system (1.5%) and gastrointestinal anomalies (1.5%) occurred with lower frequency. The finding of a solid cartilaginous trachea is particularly important because no case was diagnosed during life but rather, only at autopsy. Because cardiovascular and genitourinary anomalies occur with significant frequency, they should be considered in the workup of all Apert newborn infants. We also recommend MRI study of the trachea in any infant with signs and symptoms of lower respiratory compromise.