BackgroundTo describe, with aid of geo-mapping, the effects of a risk-based capitation model linked to caries-preventive guidelines on the polarization of caries in preschool children living in the Halland region of Sweden.MethodsThe new capitation model was implemented in 2013 in which more money was allocated to Public Dental Clinics surrounded by administrative parishes inhabited by children with increased caries risk, while a reduced capitation was allocated to those clinics with a low burden of high risk children. Regional geo-maps of caries risk based on caries prevalence, level of education and the families purchasing power were produced for 3-6-year-old children in 2010 (n = 10,583) and 2016 (n = 7574). Newly migrated children to the region (n = 344 in 2010 and n = 522 in 2016) were analyzed separately. A regional caries polarization index was calculated as the ratio between the maximum and minimum estimates of caries frequency on parish-level, based on a Bayesian hierarchical mapping model.ResultsOverall, the total caries prevalence (dmfs > 0) remained unchanged from 2010 (10.6%) to 2016 (10.5%). However, the polarization index decreased from 7.0 in 2010 to 5.6 in 2016. Newly arrived children born outside Sweden had around four times higher caries prevalence than their Swedish-born peers.ConclusionsA risk-based capitation model could reduce the socio-economic inequalities in dental caries among preschool children living in Sweden. Although updated evidence-based caries-preventive guidelines were released, the total prevalence of caries on dentin surface level was unaffected 4 years after the implementation.Electronic supplementary materialThe online version of this article (10.1186/s12903-017-0470-6) contains supplementary material, which is available to authorized users.