Background Little is known about the effects of socio-environmental factors on dental caries in different demographic situations in Asian populations. We investigated whether the nature of the association between regional socio-economic context and dental caries experience differed according to gender and age groups in Korean adults. Methods We obtained a linked data set containing individual information from the 2000 Korean National Oral Health Survey and regional information from the “Major statistical indices of Si-Gun-Gu” (city-county-ward), published by the Korean Statistical Office. We stratified participants into women and men and into four 10-year-interval age groups (19–34, 35–44, 45–54, and 55–64 years) and analysed the linked data using a multilevel analysis. In total, 5,259 individuals were included in the final study population. Results Regional socio-economic context was significantly associated with dental caries experience in men, but not in women. The patterns of the association between regional contextual variables and dental caries experience differed among age groups. People 35–44 years of age living in areas less dependent on the manufacturing industry and those 45–54 years of age living in areas where local government was relatively poor were more prone to have caries experience. Conclusions The results of this study indicated that socio-economic factors affecting residents’ dental health status may operate through different mechanisms or degrees according to geographic location, suggesting that some gender- and age-defined subgroups may be likely to benefit from different types of intervention, including the development of specific health policies.