The objective of this study was to investigate mechanisms of exercise-induced pulmonary hypertension in patients with congenital cardiac septal defects. This was a randomized, placebo controlled, crossover drug trial in a single national pediatric cardiology centre that performs congenital cardiac defect surgery. There were 14 patients with cardiac septal defects and known exercise-induced pulmonary hypertension. The intervention consisted of 50 mg oral sildenafil versus placebo. Measurements included supine bicycle exercise echocardiography and oxygen uptake. The outcome measure was right-ventricular systolic pressure as estimated by Doppler tracings of tricuspid regurgitant jet as well as systolic and diastolic longitudinal myocardial velocities by color tissue Doppler echocardiography. Sildenafil did not change exercise right-ventricular systolic pressure during exercise; however, decreased systemic systolic pressure was seen. Enhanced biventricular longitudinal function with sildenafil compared with placebo was indicated by greater tissue Doppler velocities and displacement measurements during exercise. Finally, a less steep increase of right-ventricular pressure during exercise was associated with greater left-ventricular diastolic myocardial tissue Doppler velocity. Exercise-induced pulmonary hypertension in cardiac septal defects does not seem to have a pulmonary vasoconstrictive component, but it may be related to left-ventricular filling pressure. Furthermore, sildenafil improved biventricular systolic performance in this patient group, possibly related to decreased systemic afterload.