The recent exponential increase in knowledge in genetics has revolutionized all aspects of medicine. The completion of the first draft of the human genome project has provided for clinicians a range and depth of information never before imagined. Over the last 25 years understanding the anatomical and physiological basis of a number of congenital cardiac anomalies has led to better care and outcome for the patients born with congenital cardiac defects. In the last decade the role of genes, their critical timing of expression, and understanding of important downstream pathways for optimizing normal development and control of the left right asymmetry have emerged. The progress in cardiac genetics has been supplemented by advances in cardiac imaging modalities leading to improvements in diagnosis of the cardiac anomalies. About 30% of all congenital heart diseases are associated with extra- cardiac malformations. Chromosomal anomalies are more common in patients with cardiac anomalies than the general population. Presence of facial dysmorphic features and associated extra-cardiac anomalies should alert the pediatricians to an underlying syndrome diagnosis. Newer molecular cytogenetics techniques such as fluorescence in situ hybridization (FISH) and molecular tests are now routinely utilized for confirming clinical diagnoses. In this review we have summarized clinical features and discussed the genetic basis of several syndromes (for example, 22q11 deletion syndrome, Williams syndrome, Down Syndrome, Kabuki syndrome etc.) where specific cardiac anomalies are frequently encountered. The importance of establishing an accurate clinical diagnosis cannot be over emphasized. The families need genetic counselling with accurate information on the recurrence risks. With the advent of the Internet and rapid access to information, the clinicians and the patient families can access valuable information regarding the prognosis, natural history, and clinical interventions for the affected child, and useful support groups for the family. Detection of cardiac anomalies during antenatal period warrants a genetics assessment.