Early childhood caries (ECC) are an oral health problem worldwide in children under 6 years of age. This disease of rapid development has a multifactorial etiology, and one of the possible risk factors is developmental defects of enamel (DDE), such as hypoplasia and opacities. The aim of this systematic review was to evaluate the association between DDE and ECC in children under 6 years of age. An electronic search was conducted until March 2022 using Medline (PubMed), Scopus, Science-Direct, LILACS, Web of Science, Cochrane Library, EBSCO-Host, EMBASE, and Google Scholar and complemented with a manual search, with no restrictions on language or date of publication. Longitudinal studies of children under 6 years of age with primary dentition were included. A total of 1158 studies were found, of which 651 records were reviewed by title and abstract, and 24 articles were selected for full-text evaluation. Finally, nine studies that met the selection criteria were included in the qualitative synthesis. Study quality and certainty were assessed using the Newcastle-Ottawa scale and the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) tool. Three cohort studies of good quality were included in the meta-analysis. A risk associated with DDE (RR = 1.94; 95% CI: 1.52–2.49) and a risk associated with enamel hypoplasia (RR = 5.45; 95% CI: 1.84–16.14) were found. The results for diffuse opacity (RR = 1.21; 95% CI: 0.18–8.15) and demarcated opacity (RR = 1.26; 95% CI: 0.43–3.65) were not significant. GRADE analysis presented low and very low certainty of evidence. It was concluded that there is an association between DDE and ECC. However, the results should be interpreted with caution because of the limitations of the study.The protocol for this study has been registered in PROSPERO under identification number CRD42021238919.