Background: Congenital malformations are defined as those structural, metabolic or functional defects found at birth. Aim: To study the mortality due to congenital malformations in Chile between 1969 and 1997, their type, individual, temporal and geographic variations. Material and Methods: A descriptive analisis of deaths registered by the National Statistics Institute and the Ministry of Health. Means, frequencies, raw and adjusted rates were calculated and inferences for some variables were carried out. Results: Between 1969 and 1997 ther was tendency towards a reduction in rates of mortality due to congenital malformations and an increment in their relative importance. During the period, the risk for chromosome (98%) and osteomuscular (67%) malformations increased. Men and children of less than one year had the higher risk. In 1995, 1167 deaths due to congenital malformations were registered, 90% in children of less than 5 years. Higher risks occurred in urban zones (with a rate of 8.25 per 100.000) in the third region (rate 11.59) and second region (rate 11.2). Most deaths occurred in hospitals (85%). Main causes of death were circulatory system, central nervous system and chromosome malformations. Conclusions: The differences in regional deaths due to congenital malformations suggests specific risks that deserve further study. (Rev Méd Chile 2000; 128: 392-98).