Newborn care is an important factor associated with hospitalization and neonatal mortality. To analyze factors associated with hospitalization and neonatal mortality of newborns (NBs) admitted to the Unified Health System (SUS), São Paulo, 2012. A cohort of NBs from the SUS was obtained by linking data: SUS Hospital Information System, Live Birth Information System, Mortality Information System and National Health Facility Registry. Poisson and Cox regression were performed. 16.5% (9,127) of the NBs were hospitalized, 4.7% (2,613) were admitted to a Neonatal Intensive Care Unit (NICU) and 11.8% (6,514) to a Neonatal Intermediate Care Unit (NIMCU). Maternal age ≥ 35 years (RR = 1.1, IC95% 1.1 - 1.2), inadequate prenatal care (RR = 1.2, IC95% 1.1 - 1.3), hospitalization for obstetric complications (RR = 1.1, IC95% 1.1 - 1.2), prematurity (≤ 32 weeks: RR = 1.6, IC95% 1.5 - 1.8; 32 to 36 weeks: RR = 1.7, IC95% 1.6 - 1,7), low weight (< 1,500 g: RR = 2.4, IC95% 2.1 - 2.6; 1,500 to 2,499 g: RR = 2.6, IC95% 2.5 - 2.7), APGAR 5º < 7 (RR = 1.9, IC95% 1.7 - 2.0), Cesarean section (RR = 1.1, IC95% 1.1 - 1.2) and Congenital Malformation (RR = 1.4, IC95% 1.3 - 1,5) were associated with the hospitalization of newborns. Neonatal mortality was associated with infants under 1,500 g (RR = 9.1, IC95% 6.3 - 13.1), very premature (RR = 2.6, IC95% 1.9 - 3.5), low APGAR (RR = 5.5, IC95% 4.6 - 6.7). Inadequate prenatal care, prematurity and low weight were risk factors for hospitalization and neonatal mortality.