Background Optimal utilization of dental caries data is crucial in epidemiological research of individuals with juvenile idiopathic arthritis (JIA). The aims were to: explore whether caries is more prevalent among children and adolescents with JIA compared to controls; examine presence of caries according to JIA group, socio-behavioral and intraoral characteristics, and the extent to which surface-specific caries varies between and within individuals; assess whether surface-specific caries varies according to JIA group and dentition; and investigate whether disease-specific clinical features of JIA are associated with presence of caries. Methods In this comparative cross-sectional study, calibrated dentists examined index teeth (primary 2. molars, 1. permanent molars) of 4-16-year-olds with JIA (n = 219) and matched controls (n = 224), using a detailed caries diagnosis system (including enamel caries). JIA-specific characteristics were assessed by pediatric rheumatologists and socio-behavioral information collected by questionnaires. Multilevel mixed-effect logistic regressions reporting odds ratios (OR) with 95% confidence interval (CI) were applied (caries at surface level as outcome variable). Potential confounders were adjusted for, and the effect of dependency of surface-specific caries data was estimated by calculating intra-class correlation coefficients (ICC). Results At individual level, no significant difference in caries prevalence was found between individuals with JIA and controls, regardless of inclusion of enamel caries. Proportion of enamel lesions exceeded dentine lesions. JIA was not associated with presence of caries, but in both groups, low maternal educational level was associated with presence of caries (OR: 2.07, 95% CI: 1.24-3.46). Occlusal and mesial surfaces, compared to buccal surfaces, had generally higher OR according to presence of caries than distal and lingual surfaces (ICC = 0.56). Surface-specific caries in the permanent dentition differed significantly according to group affiliation. Some JIA disease-specific variables were suggested to associate with presence of caries. Conclusions No overall difference in caries prevalence between individuals with JIA and controls was observed, but for both groups, low maternal educational level and tooth surface associated with presence of caries. Associations between JIA disease-specific variables and presence of caries cannot be excluded. Due to predominance of enamel lesions, the potential of preventative dental strategies is considerable.