Congenital heart defects (CHD) are the most common single organ malformations in humans. A comprehensive study was initiated within the Competence Network for Congenital Heart Defects to assess population-based nationwide prevalence data for Germany. Study register of demographic and medical data of live births with CHD born between July 2006 and June 2007. Seven thousand two hundred forty-five live births and infants with CHD were registered in Germany by 260 participating institutions (prevalence 107.6 per 10,000 live births). The most common lesions were ventricular septal defect, atrial septal defect and valvular pulmonary stenosis with 52.7, 18.3 and 6.6 per 10,000 live births, respectively. A single ventricle, tetralogy of Fallot and the complete transposition of the great arteries were the most common severe cardiac lesions (3.0, 2.7 and 2.3 per 10,000 live births). Parents reported that prenatal echocardiography had been performed in 53.8% of severe CHD cases with a cardiac defect detected in 77.5% of them. The reported prevalences of severe CHD are within the range of regional and European comparative data. The prenatal detection rate of severe cardiovascular malformations is comparable to contemporary European registries. Postnatal diagnosis of the CHD has been made early in life.