Abstract Objectives: to describe the prevalence of congenital malformations in live births in Recife, based on the relationship of birth and infant death data. Methods: a cross-sectional study with data from the Live Birth Information System (Sinasc) and Mortality (MIS) of residents in Recife-PE between 2013 and 2015. The deterministic linkage of deaths and live births (LB) with malformation and the prevalence rate were calculated. Results: 545 (95.1%) deaths and live births were matched. According to the Sinasc, the prevalence of congenital malformations was 10.4 per 1,000 LB. After the linkage, the rate was 12.4. Malformations of the musculoskeletal system (42.1%) among live births were high-lighted, as well as malformations of the circulatory system (35.3%) found in infant deaths. Conclusions: linkage increased the prevalence of congenital malformations in the studied cohort. This demonstrates the potential of this strategy for the monitoring of congenital malformations, which can be used to monitor infant death.