Congenital malformation is observed in about 2-5% of newborns and is a leading cause of infant mortality. The prognosis of malformation is dictated mainly by proper treatment followed by correct diagnosis at an early age. In practice, etiological consideration and classification of a malformation is critical for diagnosis. Malformations can be classified as belonged to minor or major anomaly. It is clinically important to clarify the pathogenesis of the anomalies among malformation, deformation, disruption, and dysruption. Genetic counseling aids this process by helping patients or family members understand and the nature of the malformation and risk assessment.