Background: Previous research suggests there are significant differences between socio-economic groups in prevalence and amount of decayed missing and filled primary teeth (d(3)mft). The aim of this study was to describe the variation in obvious tooth decay experience amongst 5-year olds in Scotland and to look at the association between d(3)mft and deprivation in Scotland. Methods: Data derived from 1993 to 2003 National Dental Inspection Programme were modelled using Bayesian multilevel zero-inflated Negative Binomial models, adjusting for age, sex and the deprivation. Results: Deprivation is positively and significantly associated with having d(3)mft; the odds of a child in DepCat 7 (most deprived) having d(3)mft in 1993 were 7.49 (5.0311.15) that of a child in DepCat 1 (most affluent). Inequalities in the prevalence of d(3)mft have reduced and in 2003 the odds of a child in DepCat 7 having d(3)mft were 4.60 (3.476.14) that of a child in DepCat 1. However, socio-economic inequalities in the amount of d(3)mft for those with d(3)mft have seen no reduction and have in fact increased between 1993 and 2003, with this increase approaching significance. Conclusion: While socio-economic inequalities in prevalence of children with d(3)mft have decreased in recent years, socio-economic inequalities in the amount of d(3)mft for those with d(3)mft persist. This suggests that improvements are only seen for those children with the potential for low d(3)mft. High d(3)mft persists among children from more deprived areas. The national target conceals this apparent inconsistency.