Objectives. To estimate the rate of neonatal mortality and to describe neonatal deaths in 2011 in hospitals of the Ministry of Health at Huanuco and Ucayali (Peru). Materials and methods. Cross-sectional study from September to November 2012 in Huanuco and Ucayali. Records of neonatal deaths in 2011 were reviewed from provincial municipalities, regional health directorates and four referral hospitals. To calculate mortality rates, we used the most reliable information sources by region. Reviewing 185 medical records in hospitals allowed us to describe the root causes of neonatal deaths. Results. In 2011, 10, 886 live births and 158 neonatal deaths were reported in Huanuco, with a rate of 14.5 deaths per 1000 live births. In Ucayali, 11, 441 live births and 138 neonatal deaths were reported, with a rate of 12.1 deaths per 1000 live births. Most hospital neonatal deaths occurred in the first 7 days of life (87%), in preterm infants (73.9%) and with low birth weight (67%). The most common underlying causes of neonatal deaths were infection (31.4%), congenital malformation (22.2%) and prematurity (18.9%). Conclusions. Neonatal mortality rate in the studied regions was higher than the national average. The results suggest the need for effective and comprehensive interventions during pregnancy, childbirth and the early postnatal period; this last period is the most vulnerable in the neonate.