Objective Acquired von Willebrand syndrome (AvWD) is associated with various underlying diseases, i.e. myeloproliferative disorders or aortic stenosis in adults. Reliable data on AvWD in patients with congenital heart disease (CHD) are rare. However these patients have an increased risk of bleeding when undergoing surgical or interventional procedures. The aim of our study is the prospective screening and characterization of AvWD in this setting. Methods All consecutive patients with CHD admitted to our paediatric cardiology department for surgery or cardiac catheterisation were included in the study. In addition to routine coagulation tests, levels of ristocetin cofactor, von Willebrand factor antigen, and factor VIII activity were measured. Cardiac morphological and haemodynamic evaluation was simultaneously performed. Results AvWD was detected in 11 of 80 patients (13.8%) with different forms of CHD. Three children (3.8%) with diagnosed AvWD showed clinically apparent tendency of bleeding. In one patient with surgically corrected tetralogy of Fallot and significant pulmonary artery homograft stenosis, bleeding tendency disappeared following homograft replacement. Generally no significant relationship between type of heart failure or defined haemodynamic conditions and AvWD could be observed. Conclusions Patients with CHD have an increased risk to develop AvWD. This disorder should be considered in all patients with prolonged bleeding after cardiac surgery. Although specific causes of AvWD due to congenital heart defects remain unclear, it may be improved by surgical correction of a haemodynamic abnormality. To determine the relevance of AvWD for clinical practice and to provide a better understanding of its pathogenesis further investigation is warranted.