The increasing role of genetic factors in the etiology of congenital heart defects is shown by the high frequency of genetic syndromes and extracardiac malformations in these patients. The accurate study of cardiac anatomy disclosed that peculiar morphologic subtypes of heart defects are related to specific genetic conditions. The correlation between anatomic cardiac patterns and some genetic anomalies (trisomy, deletion, mutation) suggests that specific morphogenetic mechanisms put in motion by gene(s) can result in a specific cardiac phenotype. In this review we analyze the cardiac morphology and the frequent genetic syndromes in five groups of congenital heart diseases: right-sided obstructions, left-sided obstructions, atrioventricular canal defects, ventricular septal defects, and conotruncal defects. Progress in this field is due not only to new research in molecular biology, but also to the attention of clinicians to a detailed cardiac diagnosis and to specific correlations between genotype and phenotype.