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Background: This study was undertaken in order to 1) determine the frequency of infants with major congenital malformations who are breastfed and 2) identify factors associated with initiating and early weaning of breastfeeding., Methods: We conducted a descriptive cohort study at a tertiary-care pediatric hospital. Subjects included infants <20 days of age with major congenital malformations. According to the feeding pattern, the following three groups were identified: exclusively breastfed (EB); alternating breast and formula (ABF), and exclusively formula (EF).Follow-up interviews were conducted on a monthly basis until the infants were 6 months of age. The feeding pattern was determined during each visit. Reasons for changing the breastfeeding pattern were explored., Results: A total of 120 newborns were recruited. At the time of the first interview, 29.2% were EF, 47.5% EB, and 23.3% ABF. By 6 months of age, the feeding patterns were 8.6, 18.1, and 73.3%, respectively. Median length of breastfeeding was 3 months (range: 1-6 months). The maternal prenatal decision to breastfeed (odds ratio [OR] 0.11, 95% confidence interval [95% CI] 0.02-0.52) and attendance at prenatal breastfeeding sessions (OR 0.30, 95% CI 0.17-0.87) were associated with breastfeeding initiation. Conversely, mother-child separation (OR 3.07, 95% CI 1.36-7.01) and low birth weight (OR 2.98, 95% CI 1.36-6.48) were associated with a lack of breastfeeding. The mother's sensation of low milk production was the main reason to change or to stop breastfeeding., Conclusions: In this study, breastfeeding frequency and length among infants with congenital malformations during the first 6 months of life were lower than previously published reports of breastfeeding obtained from healthy infants. Healthcare professionals must encourage breastfeeding in these infants.