The aim of this study was to investigate potential differences in caries prevalence of children from ethnic minority groups compared to native Dutch children and the influence of socio-economic status (SES) and parent-reported oral health behaviour on this association. The study had a cross-sectional design, embedded in a population-based prospective multi-ethnic cohort study. 4,306 children with information on caries experience, belonging to 7 different ethnic groups, participated in this study. The decayed, missing, and filled teeth (dmft) index was assessed at the age of 6 and categorized in two ways for analysis: children without caries (dmft = 0) versus any caries experience (dmft >0) and children without caries (dmft = 0) versus children with mild caries (dmft = 1-3) or severe caries (dmft >3). Compared to native Dutch children, children with a Surinamese-Hindustani, Surinamese-Creole, Turkish, Moroccan, and Cape Verdean background had significantly higher odds for dental caries. Especially the Surinamese-Hindustani, Turkish, and Moroccan group had significantly higher odds for severe dental caries. Household income and educational level of the mother explained up to 43% of the association between ethnicity and dental caries, whereas parent-reported oral health behaviour did not mediate the association. Alarming disparities in caries prevalence between different ethnic (minority) groups exist, which cannot be fully explained by social inequalities. Public health strategies can apply this new knowledge and specifically focus on the reduction of ethnic disparities in oral health. More research is needed to explain the high caries prevalence among different ethnic minority groups.