Abstract: Congenital anomalies are the structural and functional irregularities at birth. In this progressive study, all the neonates who are admitted to the Neonatal Intensive Care Unit during the three year period from 1st June 2017 to 31 May 2020. Aim: The study aims to examine the prevalence, type, and epidemiological factors of congenital anomalies among the population of Ladakh India. Subject and methods: All the neonates during the study period were examined by pediatrics and questionnaire filled by the consent of the family. A total of 936 parents of neonates was agreed to participate in this study and among them, 524 are male neonate and 412 was female. Results: Four and a half percent were diagnosed as being congenital malformed and the common system affected by congenital anomalies in the digestive system followed by the mucso-skeletal system. In this study, based on the logistic regression consanguineous marriage with OR of 9.862 (4.221; 23.041), P= <0.001, familial congenital anomalies in the family with OR of 17.008 (4.343; 66.606), P=0.001, an anaemic mother with OR of .124 (.029; .538). P = .005, Apgar score with .033 (.016: .067), P-value of <0.001 and paternal smoking with OR of 13.305 (5.558: 31.854) with P value of <0.001 had shown a very good significant correlation with the congenital anomalies. Conclusion: The occurrence and distribution of congenital anomalies in Ladakh were reported. More active prenatal screening and the possible role of genomics study are major importance to uncovering the susceptibilities.