Background. Socioeconomic differences in oral health have been reported in many countries. Poverty and social exclusion are two commonly used indicators of socioeconomic position in Latin America. The aim of this study was to explore the associations of poverty and social exclusion with dental caries experience in 12-year-old children. Methods. Ninety families, with a child aged 12 years, were selected from 11 underserved communities in Lima (Peru), using a two-stage cluster sampling. Head of households were interviewed with regard to indicators of poverty and social exclusion and their children were clinically examined for dental caries. The associations of poverty and social exclusion with dental caries prevalence were tested in binary logistic regression models. Results. Among children in the sample, 84.5% lived in poor households and 30.0% in socially excluded families. Out of all the children, 83.3% had dental caries. Poverty and social exclusion were significantly associated with dental caries in the unadjusted models (p = 0.013 and 0.047 respectively). In the adjusted model, poverty remained significantly related to dental caries (p = 0.008), but the association between social exclusion and dental caries was no longer significant (p = 0.077). Children living in poor households were 2.25 times more likely to have dental caries (95% confidence interval: 1.24; 4.09), compared to those living in non-poor households. Conclusion. There was support for an association between poverty and dental caries, but not for an association between social exclusion and dental caries in these children. Some potential explanations for these findings are discussed. © 2009 Delgado-Angulo et al; licensee BioMed Central Ltd.