Objective The aim of this study was to describe the caries experience, prevalence and distribution related to tooth type and surfaces in the primary and permanent dentition in children and adolescents in Denmark in 2012. In addition, to examine if explanatory factors influence the inter-municipality variation in caries experience. Materials and methods Data was collected in the public Child Dental Health Service. In total, 5636 caries registrations on 3-, 9-, 15- and 18-year-olds were collected in 35 of the 98 Danish municipalities. Caries experience was expressed by mean def-s/DMF-S and caries prevalence by def-s = 0/DMF-S = 0. Inter-municipality variations were illustrated. Multivariate regression analyses were applied to assess the influence of fluoride concentration in drinking water, proportion of immigrants and personal income on the inter-municipality variation in mean def-s/DMF-S. Results Only 4.6% of 3-year-olds had def-s (mean = 0.25), compared to 44.9% of 9-year-olds (mean = 3.07), primarily located occlusally and interproximally on the primary molars. Mean DMF-S for the 9-, 15- and 18-year-olds were 0.27, 1.97 and 4.40, respectively. Caries were primarily located occlusally and in pits on the permanent molars, which also showed high frequencies of sealings. Mean def-s/DMF-S showed substantial inter-municipality variations, while the caries location in both dentitions was rather stable. The three background factors explained less than 25% of the variation in mean def-s/DMF. Conclusions The caries distribution within the primary and permanent dentition among 3-, 9-, 15- and 18-year-olds followed definite patterns concerning location on teeth and surfaces. Background factors only explained a minor part of the variation.