Cost effectiveness is becoming an increasingly important factor for stakeholders faced with decisions about adding a new vaccine into national immunization programmes versus alternative use of resources. Evaluating cost effectiveness, taking into account the relevant biological, clinical, epidemiological and economic factors of a vaccination programme, generally requires use of a model. This review examines the modelling approaches used in cost-effectiveness analyses (CEAs) of vaccination programmes.After overviewing the key attributes of models used in CEAs, a framework for categorising theoretical models is presented. Categories are based on three main attributes: static/dynamic; stochastic/deterministic; and aggregate/individual based. This framework was applied to a systematic review of CEAs of all currently available vaccines for the period of 1976 to May 2007. The systematic review identified 276 CEAs of vaccination programmes. The great majority (83%) of CEAs were conducted in the setting of high-income countries. Only a few vaccines were widely studied, with 57% of available CEAs being focused on the varicella, influenza, hepatitis A, hepatitis B or pneumococcal vaccine. Several time trends were evident, indicating that the number of vaccine CEAs being published is increasing; the main health outcome measures are moving away from the number of cases prevented towards quality-adjusted and unadjusted life-years gained, and more complex models are beginning to be used. The modelling approach was often not adequately described. Of the 208 CEAs that could be categorized according to the framework, around 90% were deterministic, aggregate-level static models. Although a dynamic transmission model is required to account for herd-immunity effects, only 23 of the CEAs were dynamic. None of the CEAs were individual based. To improve communication about the cost effectiveness of vaccination programmes, we believe the first step is for analysts to be more transparent with each other. A clear description of the model type using consistent terminology and justification for the model choice must begin to accompany all CEAs. As a minimum, we urge modellers to provide an explicit statement about the following attributes: static/dynamic; stochastic/deterministic; aggregate/individual based; open/closed. Where relevant, time intervals (discrete/continuous) and (non)linearity should also be described. Enhanced methods of assessing model performance and validity are also required. Our results emphasize the need to improve modelling methods for CEAs of vaccination programmes; specifically, model choice, construction, assessment and validation.