The coastal regions of some states (Kerala, Tamil Nadu, Andhra Pradesh and Orissa) in India are known to have plenty of thorium-rich minerals, therefore possess high external gamma radiation fields, and are identified as Natural High Background Radiation Areas. There are concerns about congenital malformations due to the high background radiation prevailing in the region. Therefore, scientists find interest to study the possible biological effects of low-level exposures on the local populace who are living with generations under these extraordinary radiation fields. The present study is an attempt to find the correlation between the incidences of certain congenital malformations through a 1:3 matched case-control study. A total of 75 subjects (58 mental retardation cases and 17 Cleft lip/palate cases) along with 225 controls were selected for the investigations. Indoor and outdoor gamma dose rates were measured using a halogen-quenched GM tube-based survey meter, while the indoor inhalation dose rates were measured based on the radon and progeny measurements using the twin cup dosimeters equipped with LR-115 Type II solid-state nuclear track detectors. Conditional logistic regression analysis was used to find out the correlation between the radiation dose with congenital malformation. This study found an insignificant risk of cleft lip/palate (but not for mental retardation) from the exposures to natural high external gamma radiation fields in the study area. Therefore, the results of the investigation indicate no explicit risk of congenital malformations by the high background natural radiation prevailing in the region.