This review investigated whether mode of delivery influences the colonization of infant’s oral cavity and the risk of early childhood caries (ECC). The search strategy included systematic searching of electronic databases (Web of Science and PubMed) for articles published (1995–2015) and hand searching of references lists. Outcomes of interest were the presence of oral caries-related microorganisms, oral species considered protective against caries, and dental caries. Other outcomes included severity of dental caries, dental claims, and age at first dental visit. Study quality was assessed using the EPHPP tool. For each study, we present odds ratios and respective 95% confidence intervals for the association between these outcomes and the mode of delivery. Fourteen studies were identified. In 5 out of 8 studies addressing oral colonization, children born by cesarean section were less likely to harbor caries-related microorganisms as well as protective bacteria against caries and acquired caries-related microorganisms earlier, when compared with vaginally delivered children. No consistent results were obtained for the association between mode of delivery and dental caries. Although there were differences in oral colonization by mode of delivery, it seems that other determinants rather than mode of delivery could be major contributors to the development of ECC.