Background The information on dental caries experience and its determinants in Central Asia is limited. The aim of the present study was to provide estimates of the mean levels, prevalence and severity of dental caries, and to identify the factors associated with these characteristics in the population of school-aged children from four regions in Kazakhstan.Methods We examined 2149 schoolchildren aged 11–15 years from 4 regions of Kazakhstan. The overall response rate was 68%. Dental caries experience was assessed clinically, and standardized questionnaire was used to gather sociodemographic and oral health behavior information. Caries experience was measured by using DMFT (decayed, missing, and filled teeth) index. Negative binomial hurdle regression model was used to assess the relationship between the caries experience and covariates.Results The overall prevalence of dental caries was 74%, obvious decayed teeth was found in 44% of subjects, while only 6% had missing teeth and 24% had their teeth treated. The mean DMFT index was 2.48 among 12-year-olds and 3.9 among 15-year-olds. There were large differences of dental caries experience between the regions, with all indicators (decayed, missed and filled teeth) being less favourable in Semey region. The caries prevalence experience in the studied population was associated with higher age, geographic region, ethnicity, mother’s education, material deprivation, frequent consumption of sugar-added drinks, age of start brushing the teeth and dental attendance pattern. Age, region, ethnicity, dietary habits and dental attendance pattern were found to be significantly associated with the predicted degree of caries experience among those with caries experience.Conclusions The high prevalence of dental caries and large differences in caries indices between the regions in Kazakhstan might be related to rapid westernization in the Central Asian region and associated nutrition transition. Also, the increasing burden of untreated caries in less advantaged populations was observed. Parent education and material deprivation may be a very important determinants of the oral health among adolescents in Kazakhstan.