Congenital malformations are single or multiple defects of the morphogenesis of organs or body districts identifiable at birth or during the intrauterine life. Their global birth prevalence is about 2-3%. Both genetic and environmental factors, as well as their combination in a multifactorial contest, may induce congenital defects. Congenital malformations may be classified on the basis of clinical, etiologic as well as pathogenetic criteria. Relevant diagnostic and therapeutic tools have been progressively improving in the last decades, contributing to a better identification and a reduction of long-term morbidity and mortality of these patients. A correct identification of a congenital defect is the first step in order to offer a helpful genetic counseling to the parental couple. Because of their increasing life expectancy, congenital malformations represent today a major issue in the health services for the amount of resources they need for the requested multidisciplinary assistance.