Ayurveda states that congenital disorders can be due to defect in germ cells or somatic cells in the intra-uterine environment. The interaction of germ cell genotype, geo-climatic & uterine factors, mother's diet & activities as well as the nature of Panchamahabhoota in the environment at the time of fertilization, determine the Prakriti (phenotype). The unhealthy state of either factor can affect the prakriti of the fetus & even result in congenital diseases. Ayurveda supports different clan (Atulya gotra) marriage, as consanguinity increases the risk of congenital anomalies. It is mentioned that a seed cultivated in a healthy field only can yield supreme variety of crop; the procedures to make the reproductive system healthy may prevent the occurrence of congenital disorders. Ayurgenomicsis is a phenomenon where, by personalized health care approach before conception may help to prevent the congenital anomalies to some extent. The present review aims to highlight Ayurgenomics in predictive, preventive and personalized aspects of congenital anomalies. Thus, Ayurgenomics may be a new facet for the preventive aspect of congenital disorders.