Abstract Background To investigate the prevalence and patterns of breastfeeding at discharge and in the first six months of life in a high-risk fetal, neonatal and child referral center. Methods Prospective, longitudinal study that included the following three steps: hospital admission, first visit after hospital discharge and monthly telephone interview until the sixth month of life. The total number of losses was 75 mothers (7.5%). Exposure variables were sorted into four groups: factors related to the newborn, the mother, the health service and breastfeeding. The dependent variable is breastfeeding as per categories established by the WHO. All 1200 children born or transferred to the high-risk fetal, neonatal and child referral center, within a seven-day postpartum period, from March 2017 to April 2018, were considered eligible for the study, and only 1003 were included. The follow-up period ended in October 2018. For this paper, we performed an exploratory analysis at hospital discharge in three stages, as follows: (i) frequencies of baseline characteristics, stratified by risk for newborn; (ii) a multiple correspondence analysis (MCA); and (iii) clusters for variables related to hospital practice and exclusive breastfeeding (EBF). Results The prevalence of EBF at hospital discharge was 65.2% (62.1–68.2) and 20.6% (16.5–25.0) in the six months of life. Out of all at-risk newborns, 45.7% were in EBF at discharge. The total inertia corresponding to the two dimensions in the MCA explained for 75.4% of the total data variability, with the identification of four groups, confirmed by the cluster analysis. Discussion Our results suggest that robust breastfeeding hospital policies and practices influence the establishment and maintenance of breastfeeding in both healthy and at-risk infants. It is advisable to plan and implement additional strategies to ensure that vulnerable and healthy newborns receive optimal feeding. It is necessary to devote extra effort particularly to at-risk infants who are more vulnerable to negative outcomes. Conclusion At-risk newborns did not exclusively breastfeed to the same extent as healthy newborns at hospital discharge. A different approach is required for at-risk neonates, who are more physically challenged and more vulnerable to problems associated with initiation and maintenance of breastfeeding.