Background. Discontinuous pulmonary arteries have been considered a rare complication of systemic-to-pulmonary shunt operations. We report a series of children who spontaneously acquired pulmonary artery discontinuity. Methods. All children from 1989 through 1995 with congenital pulmonary atresia were reviewed. Results. Pulmonary artery discontinuity developed in 29% (15 patients), none related to shunt operation. In 6 of 15 patients, the neonatal angiogram showed a pattern that seemed to predict subsequent discontinuity; in 9 of 15, pulmonary arteriography was normal at birth. Two clinical patterns were identified: an early rapid acquisition of discontinuity within hours to days, and a delayed, more subtle development that occurred over months. Eight of 15 have died. Pathologic studies in 6 children showed ductal tissue extending along and into the pulmonary artery wall as well as intimal hypertrophic reaction and maladaptive remodeling. Conclusions. Children with congenital pulmonary atresia may experience spontaneous acquisition of pulmonary artery discontinuity. Ductal tissue is responsible for local pulmonary artery distortion and discontinuity; this may be exacerbated by previous prostaglandin E 1 administration. Clinical algorithms are suggested for patients with pulmonary atresia.