The use of modelling in economic evaluation is widespread, and it most often involves synthesising data from a number of sources. However, even when economic evaluations are conducted alongside clinical trials, some form of modelling is usually essential. The aim of this article is to review the handling of uncertainty in the cost-effectiveness results that are generated by the use of decision-analytic-type modelling. The modelling process is split into a number of stages: (i) a set of methods to be employed in a study are defined, which should include a 'reference case' of agreed methods to enhance the comparability of results; (ii) the clinical and demographic characteristics of the patients the model relates to should be specified as carefully as in any experimental study; and (iii) the data requirements of the model should be estimated using the principles of Bayesian statistics, such that prior distributions are specified for unknown model parameters. Monte Carlo simulation can then be employed to sample from these prior distributions to obtain a distribution of the cost effectiveness of the intervention. Such probabilistic analyses are related to parameter uncertainty. In addition, modelling uncertainty is likely to add a further layer of uncertainty to the results of particular analyses.