Pharmacoeconomic evaluations are important elements in the decision making process, and decision tree analyses are statistical models that analyse both clinical and economic consequences of medical actions. Using one theoretic model, key confounding variables were identified that constituted a standardised framework for economic evaluation of schizophrenia management. The extent to which they were included in several previously published schizophrenia models was appraised. Five different models were developed, and a systematic review of schizophrenia modelling studies was conducted. Results indicate that atypical antipsychotics may be more or less cost-effective depending upon whether key confounding variables were taken into account, but vigilance is warranted when assessing data because serious discrepancies can occur between different methods of analysis. A need for standardised schizophrenia pharmacoeconomic models exists. Additionally, social rehabilitation should be considered because this may also influence outcomes. Standardising modelling techniques will facilitate adherence to guidelines issued by decision makers.