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Background: Congenital heart diseases are the most common type of congenital defects, and account for more deaths in the first year of life than any other condition, when infectious etiologies are ruled out., Objectives: To evaluate survival, and to identify risk factors in deaths in newborns with critical and/or complex congenital heart disease in the neonatal period., Methods: A cohort study, nested to a randomized case-control, was performed, considering the Confidence Interval of 95% (95% CI) and significance level of 5%, paired by gender of the newborn and maternal age. Case-finding, interviews, medical record analysis, clinical evaluation of pulse oximetry (heart test) and Doppler echocardiogram were performed, as well as survival analysis, and identification of death-related risk factors., Results: The risk factors found were newborns younger than 37 weeks (Relative Risk - RR: 2.89; 95% CI [1.49-5.56]; p = 0.0015), weight of less than 2,500 grams (RR: 2.33 [; 95% CI 1.26-4.29]; p = 0.0068), occurrence of twinning (RR: 11.96 [95% CI 1.43-99.85]; p = 0.022) and presence of comorbidity (RR: 2.27 [95% CI 1.58-3.26]; p < 0.0001). The incidence rate of mortality from congenital heart disease was 81 cases per 100,000 live births. The lethality attributed to critical congenital heart diseases was 64.7%, with proportional mortality of 12.0%. The survival rate at 28 days of life decreased by almost 70% in newborns with congenital heart disease. The main cause of death was cardiogenic shock., Conclusion: Preterm infants with low birth weight and comorbidities presented a higher risk of mortality related to congenital heart diseases. This cohort was extinguished very quickly, signaling the need for greater investment in assistance technology in populations with this profile.