OBJECTIVES: Early childhood caries (ECC) is a highly prevalent disease. Breastfeeding is a beneficial feeding method, but existing studies lack consensus on its association with the occurrence of ECC. This study aimed to analyse the effect of breastfeeding on ECC occurrence and possible microbiological mechanisms. METHODS: The participants included in this prospective study were divided into a bottle-feeding group and an exclusive breastfeeding group immediately after birth. At the age of two, saliva and dental plaque were collected to test the oral pH and microbial count. At the age of three, the primary dentition were examined for caries. Questionnaires were distributed to the infants' mothers before enrolment and after observation. Potential risk factors affecting ECC occurrence were screened and further clarified. RESULTS: The incidence of ECC in the bottle-feeding group was 63.5%, whereas that in the breastfeeding group was 54.1% (P <
0.05). In addition, the incidence rates of severe ECC (S-ECC) in the nonexposure group and the exposure group were 28.7% and 22.2%, respectively (P <
0.05). Breastfeeding reduced the incidence of ECC (OR = 0.63, 95% CI = 0.46-0.86) and S-ECC (OR = 0.70, 95% CI = 0.49-0.99). In addition, feeding and dietary habits also had a significant effect on ECC occurrence. Breastfeeding might affect ECC occurrence by altering the microbial count of plaque and saliva, as well as the proportion of Streptococcus mutans. CONCLUSION: Exclusive breastfeeding for six months after birth is a protective factor against ECC at the age of three. CLINICAL SIGNIFICANCE: Exclusive breastfeeding may decrease the later occurrence of ECC. Medical workers, including dentists, are responsible for promoting the initiatives on breastfeeding and providing mothers or other caregivers with accurate and up-to-date evidence-based information.