Heart development consists in a group of complex and specific morfogenetic interactions, that requires the proper activity of each factor implicated in this process. Congenital heart defects (CHD) are a group of multifactorial complex diseases with environmental and genetic factors playing important roles. There is not an exact relation between molecular mechanisms and morphological defects in CHD, because in most of the cases the proper development of an anatomical structure implies the adequate function of several pathways that may depend of the action of different genes. This review summarizes the genetic factors implied in the normal heart development and the most common gene mutations associated with CHD.