Previous research suggests there are significant differences between urban and rural areas in Scotland for health outcomes including heart disease, cancer and self reported health. The aim of this study was to describe the contemporary urban/rural variation in obvious decay experience amongst 5-year-olds in Scotland. Scotland was split into 6 geographies, ranging from 'The 4 Cities' (Glasgow, Edinburgh, Dundee and Aberdeen) to 'Remote Rural' areas. Data derived from the 2007/08 National Dental Inspection Programme, representative of the whole of Scotland, were modelled using Bayesian multilevel zero-inflated Negative Binomial and multilevel Poisson modelling, adjusting for age, sex and deprivation. The outcome variables modelled were d(3)mft (carious, extracted or filled deciduous teeth), d(3)t (carious teeth), mt (missing teeth, extracted due to caries) and ft (filled teeth). The proportion of 5-year old children in Scotland with d(3)mft = 0 was 58% in 2008. Adjusting for age and sex, the odds of a child in a Remote Rural area having d(3)mft>0 was 0.52 that of a city dweller. However, when deprivation was included in the model, the odds of having d(3)mft >0 rose to 0.74. The odds of d(3)mft>0 in 'Accessible Rural' areas also remained significantly lower than in the 4 Cities after adjustment for deprivation. For those with d(3)mft>0, the relative risk of additional d(3)mft was also significantly lower in Remote Rural areas, however this was explained by deprivation, while in Accessible Rural areas this remained significant even after adjustment for deprivation. The odds of having any extractions was lower in Rural areas, even after adjustment for deprivation, while the Care Index (ft/d(3)mft) was higher in Remote Towns. Deprivation, therefore, accounted for much but not all of the geographical difference in d(3)mft which exist in Scotland. Children in Remote and Rural areas appear to have better dental health and a higher proportion of filled teeth when compared with those living in Cities. Possible reasons for these differences and recommendations for future research are discussed.