BACKGROUND: Few studies have assessed the effect of breastfeeding, bottle feeding, and abstract sugar consumption on children’s dental caries. We investigated whether the duration of breastfeeding is a risk factor for dental caries in the primary dentition, independently of sugar consumption. METHODS: An oral health study (n = 1303) nested in a birth cohort study was carried out in southern Brazil. The average number of decayed, missing, and filled primary tooth surfaces (dmfs) and severe early childhood caries (S-ECC: dmfs ≥6) were investigated at age 5 years. Breastfeeding was the main exposure collected at birth and at 3, 12, and 24 months of age. Data on sugar consumption were collected at 24, 48, and 60 months of age. Marginal structural modeling was used to estimate the controlled direct effect of breastfeeding (0–12, 13–23, and ≥24 months) on dmfs and on S-ECC. RESULTS: The prevalence of S-ECC was 23.9%. The mean number of dmfs was 4.05. Children who were breastfed for ≥24 months had a higher number of dmfs (mean ratio: 1.9; 95% confidence interval: 1.5–2.4) and a 2.4 times higher risk of having S-ECC (risk ratio: 2.4; 95% confidence interval: 1.7–3.3) than those who were breastfed up to 12 months of age. Breastfeeding between 13 and 23 months had no effect on dental caries. CONCLUSIONS: Prolonged breastfeeding increases the risk of having dental caries. Preventive interventions for dental caries should be established as early as possible because breastfeeding is beneficial for children’s health. Mechanisms underlying this process should be investigated more deeply.