When a new drug is introduced to the market, the availability of head-to-head data for comparisons of annual cost and health outcomes with other drugs already on the market is usually insufficient. When only limited head-to-head data are available, one alternative is to perform preliminary modeling using data from the best available studies. In this paper, we synthesise data from the most comparable available studies to create a model to compare the annual costs and health outcomes when initiating treatment for schizophrenia with one of two antipsychotic drugs: olanzapine, which was launched in the United States (US) market in September 1996, and ziprasidone, which was approved by the US Food and Drug Administration (FDA) in February 2001. Annual treatment costs were determined by response and relapse rates as well as acquisition costs. The results indicate similar annual treatment costs (US$48,676 for olanzapine; US$48,873 for ziprasidone), despite the lower drug acquisition cost for ziprasidone. Annual health outcomes differed between the olanzapine and ziprasidone groups with 23.5% and 25.2% relapsed, 36.7 and 37.4 hospital days, and 60.0 and 60.1 EPS days in the olanzapine and ziprasidone groups respectively. A head-to-head naturalistic trial is needed to validate the results of this modeling exercise.