Clinical studies of dental caries experience generate multiple outcome data for each participant, with information collected for each individual tooth surface. This paper investigates multilevel modelling as a method of analysis for dental caries data, allowing for full use of the data collected at surface level. Data from a clinical trial of a caries preventive agent in adolescents are modelled. The effect of tooth position within the mouth on the development of dental caries is investigated, with the results showing the importance of differentiating between the upper and lower arches, when modelling the probabilities of caries developing on teeth. Calculation of the intracluster correlation using the threshold model is suggested for use in multilevel logistic regression modelling of caries data. This model, which assumes that a dichotomous outcome is based on an underlying continuous variable with a threshold point where the outcome changes from zero to one, is identified to be appropriate for the analysis of caries which is a continuous process, but is only identified as present in a clinical trial when it has reached a certain level of severity.