Objectives. To study the prevalence and the pattern of major congenital malformations and its contribution to the overall perinatal morbidity and mortality. Methods. It is a retrospective population based study. It includes all major congenital malformations in newborns during 1993-2012. The data was collected from the birth register, the neonatal admission register and the individual patient records at the Queen Elizabeth Hospital where over 90% of deliveries take place and it is the only facility for the care of sick newborns in this country. Results. The overall prevalence of major congenital malformations among the live births was 59/10,000 live births and that among the stillbirths was 399/10,000 stillbirths. Circulatory system was the most commonly affected and accounted for 20% of all the major congenital malformations. Individually, Down syndrome (4.1/10, 000 live births) was the commonest major congenital malformation. There was a significant increase in the overall prevalence during the study period. Major congenital malformations were responsible for 14% of all neonatal death. Conclusions. Less than 1% of all live newborns have major congenital malformations with a preponderance of the malformations of the circulatory system. Major congenital malformations contribute significantly to the overall neonatal morbidity and mortality in this country.