Objectives. To determine the frequency and clinical features of newborns with congenital malaria in the Hospital de Apoyo of Iquitos in the Peruvian Amazon. Materials and methods. Descriptive, prospective and cross-sectional study. From January 2011 to December 2013, 14.017 newborns and their mothers were studied, of whom 52 carriers of gestational malaria were selected while their infants were hospitalized in the Neonatology Unit, and underwent clinical assessment and laboratory studies. Results. Gestational malaria frequency was 0.4% and a proportion of 9.6% of congenital malaria. Plasmodium vivax was found in 80% of cases of gestational malaria and in 60% of congenital malaria. A case of fetal death with positive thick blood smear for Plasmodium falciparum was observed. The clinical presentation in newborns was fever, hypoactivity, irritability and poor suction. Conclusions. The presence of congenital malaria in infants born to mothers with gestational malaria is documented. The clinical picture resembled neonatal sepsis. Early diagnosis of congenital malaria and timely treatment present with good evolution.