Outcome data from dental caries clinical trials have a naturally hierarchical structure, with surfaces clustered within teeth, clustered within individuals. Data are often aggregated into the DMF index for each individual, losing tooth- and surface-specific information. If these data are to be analysed by tooth or surface, allowing exploration of effects of interventions on different teeth and surfaces, appropriate methods must be used to adjust for the clustered nature of the data. Multilevel modelling allows analysis of clustered data using individual observations without aggregating data, and has been little used in the field of dental caries. A simulation study was conducted to investigate the performance of multilevel modelling methods and standard caries increment analysis. Data sets were simulated from a three-level binomial distribution based on analysis of a caries clinical trial in Scottish adolescents, with varying sample sizes, treatment effects and random tooth level effects based on trials reported in Cochrane reviews of topical fluoride, and analysed to compare the power of multilevel models and traditional analysis. 40,500 data sets were simulated. Analysis showed that estimated power for the traditional caries increment method was similar to that for multilevel modelling, with more variation in smaller data sets. Multilevel modelling may not allow significant reductions in the number of participants required in a caries clinical trial, compared to the use of traditional analyses, but investigators interested in exploring the effect of their intervention in more detail may wish to consider the application of multilevel modelling to their clinical trial data.