The purpose of this study was to assess the longitudinal relationships between enamel hypoplasia and caries experience of primary second molars. The study sample was 491 subjects who received dental examinations at both age 5 and 9 by the calibrated examiners. Four primary second molars (n = 1,892) were scored for the presence of enamel hypoplasia for each participant. Caries presence and number of decayed and filled surfaces (dfs) were determined at age 5 and 9. The relationships between enamel hypoplasia and caries experience were assessed. Among primary second molars, 3.9% of children and 1.7% of primary second molars had enamel hypoplasia. At age 5, 36.8% of children with hypoplasia had caries, while 16.9% of children without enamel hypoplasia had caries. At age 9, the corresponding numbers were 52.6% for children with hypoplasia and 34.5% for children without hypoplasia, respectively. At the tooth level, for age 5, 28.1% of teeth with hypoplasia had caries (mean dfs = 0.40), and 7.6% of teeth without hypoplasia had caries (mean dfs = 0.11). At age 9, the corresponding numbers were 41.9% (mean dfs = 0.76) for teeth with hypoplasia and 18.3% (mean dfs = 0.34) for teeth without hypoplasia. In multivariable logistic regression analyses, teeth of subjects with enamel hypoplasia had a significantly higher risk for caries at age 5 and 9 after controlling for other risk factors. Enamel hypoplasia appears to be a significant risk factor for caries and should be considered in caries risk assessment.