Introduction: The association between breastfeeding status and early childhood caries (ECC) remains inconclusive. Few studies evaluate the breastfeeding status including both duration and exclusivity according to the WHO recommendations on breastfeeding. This study aimed to investigate the association between breastfeeding status and ECC. Methods: This prospective cohort study comprised 3,666 children whose breastfeeding status was precisely evaluated. Poisson regression models and multivariable linear regression models were employed to analyze the associations of breastfeeding status with risk of ECC, and mean decayed, missing, and filled primary tooth surfaces (dmfs) in 3-year-old children, respectively. The data were collected from 2014 to 2020, and the analysis was conducted in 2023. Results: The prevalences of ECC in offspring breastfed for <6 months, 6–11 months, 12–24 months, and >24 months were 9%, 12%, 17%, and 23%, respectively. Offspring breastfed for 12–24 months and over 24 months had a 1.82 times (95% CI, 1.40–2.37; p < 0.001) and 2.48 times (95% CI, 1.63–3.75; p < 0.001) higher risk of ECC, compared to those breastfed for less than 6 months. Offspring breastfed for 12–24 months showed a mean dmfs increase of 0.32 (95% CI, 0.21–0.44; p < 0.001), while those breastfed for over 24 months had a mean dmfs increase of 0.51 (95% CI, 0.27–0.74; p < 0.001), compared to those breastfed for less than 6 months. Among offspring breastfed for over 24 months, those exclusively breastfed for at least 6 months had significantly lower mean dmfs compared to those exclusively breastfed for less than 6 months (p for heterogeneity = 0.003). A significant interaction was observed between breastfeeding duration and exclusive breastfeeding duration on the association with mean dmfs (p for interaction <0.001). Conclusion: Our findings suggest that breastfeeding for over 12 months was associated with increased risk of ECC. Preventive interventions for dental caries should be implemented as early as possible, as breastfeeding is beneficial to children’s health. The associations between breastfeeding duration and exclusivity with ECC should be investigated more thoroughly, particularly with adjustments for accurately measured sugar consumption.

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