1. Eleven infants and children (mean age 4.3 years, range 0.2-12 years) with pulmonary vascular disease secondary to congenital cardiac anomalies (n = 6) or bronchopulmonary dysplasia (n = 5), were studied during cardiac catheterization while ventilated on 100% oxygen. 2. All had a raised pulmonary vascular resistance (mean 11.8 units, range 4.1-26.0 units, normal value less than 3 units) and a raised anatomical intrapulmonary right to left shunt (mean 22%, range 8-50%, normal value less than 5%). The elevated shunt was attributed to the effects of 100% oxygen and general anaesthesia causing alveolar collapse, with only partial compensation for impairment of gas exchange by compensatory local hypoxic vasoconstriction. 3. When prostacyclin was infused, pulmonary vascular resistance fell by 3.2 +/- 1.8 units (mmHg litre-1 min m2), and pulmonary blood flow rose by 1.0 +/- 0.7 litre min-1 m-2 (mean +/- 95% confidence intervals). 4. Intrapulmonary right to left shunt fraction increased in eight of 11 patients, with a maximal rise for the group of 5.9 +/- 4.6% (mean +/- 95% confidence intervals). However, even at doses of prostacyclin sufficient to cause systemic vasodilatation and tachycardia, there was no evidence for a selective increase in shunt fraction. 5. We suggest that studying the effects of therapeutic interventions on intrapulmonary shunt fraction may be a useful model in vivo of human hypoxic pulmonary vasoconstriction.