The benefits of breastfeeding are well established, but literature is scarce when it comes to newborns with anomalies. This study used a cross-sectional analysis of a prospective cohort study with 1003 neonates enrolled from March 2017 to April 2018 to estimate the prevalence of perinatal morbidities, congenital malformation and breastfeeding at hospital discharge at a national referral center for fetal, neonatal and infant high risk. The prevalence of congenital malformations was 189 (18.8%). Most infants were breastfeeding at hospital discharge, from which exclusive breastfeeding was most prevalent among infants with malformation of abdominal wall, limbs, urinary tract and others. There is great potential to increase exclusive breastfeeding rates for newborns with perinatal morbidities and congenital malformations. For that, it is necessary to implement public programs and policies to support breastfeeding within high-risk hospitals, as well as training for specific abilities to manage breastfeeding practice.