AbstractTo determine the infant mortality of newborns with 1- and 5-min Apgar scores of 0–3.Population cohort study with neonates with birth weight ≥400 g, gestational age ≥22 weeks and 1- and 5-min Apgar scores of 0–3, without malformations, born in São Paulo State (Brazil) from January 2006 to December 2007. Apgar scores were confirmed in the original certificates of live births and/or medical records. During this period, among 1,027,132 live births, 1640 met the study criteria, with an incidence of 1.6 per 1000 live births. When the 5-min Apgar score was 0, 1, 2 and 3, the infant mortality rate was 97%, 94%, 64% and 47%, respectively. Risk factors associated with infant deaths were 5-min Apgar score of 0 or 1 [odds ratio (OR) 16.6, 95% confidence interval (CI) 11.1–24.8], birth weight <2500 g (OR 7.5, 95% CI 5.7–9.8), birth at hospitals outside the state capital (OR 1.7, 95% CI 1.3–2.3), in private or charitable hospitals (OR 1.6, 95% CI 1.2–2.0), and during the night shift (OR 1.3, 95% CI 1.0–1.7).For infants with 1- and 5-min Apgar scores of 0–3, the infant mortality is high. Besides the biological variables associated with the chance of dying, the organization of the perinatal care influences the outcome.