Transposition of the great arteries is frequently complicated by the early onset of pulmonary vascular disease. It is difficult to measure pulmonary blood flow by the Fick principle because the pulmonary arteriovenous oxygen content difference is small and bronchial blood flow is increased in this condition. In eight patients (mean age 7.7 years, range 3 months to 29 years) with transposition of the great arteries mass spectrometry was used to measure oxygen uptake and predict pulmonary end capillary blood oxygen content. The effects of the bronchial circulation were studied by computer modelling. There was close agreement between pulmonary end capillary and pulmonary vein blood oxygen contents but the resultant percentage difference in arteriovenous content difference was significant (mean (SE of difference)) (14.5(3.8)%). The effect of the bronchial circulation was to give spuriously high estimates of pulmonary blood flow. The error was greatest when oxygen consumption was low and aortic blood was very desaturated.