Objective: To compare one-year post treatment costs across alternative antipsychotics in the treatment of schizophrenia. Methods: Data from a commercial health plan from July 1, 2003 to June 30, 2006 were used to identify non-institutionalized patients with schizophrenia (ICD-9 codes 295.xx) who initiated treatment a typical antipsychotic (TAP), atypical antipsychotic (AAP: aripiprazole, olanzapine, quetiapine, risperidone or ziprasidone), mood stabilizer or antidepressant. Episodes were divided into three categories: restarting treatment after a break in drug therapy >15 days with the drug used in the previous episode, switching therapy with or without a break in treatment, and augmentation therapy. First observed episodes were excluded from the analysis due to uncertainty concerning the patient's prior treatment history. A total of 21,876 episodes were included in the analyses using ordinary least squares (OLS) regression models of post-treatment costs adjusting for age, gender, geographic region, drug use history, prior medical care use, schizophrenia diagnosis and co-morbid medical conditions Results: Average total cost measured across all episodes ranged from $22,804 for TAPs to $32,357 for mood stabilizers. Augmentation episodes were estimated to be significantly more costly than switching episodes (+$4222, p<0.0001) or restart episodes (+$6970, p<0.0001). There is considerable variability in total cost across medications. However, in this commercially insured population, there is no significant difference in post-treatment costs between patients receiving individual AAPs and TAP. Patients with schizophrenia treated with mood stabilizers were significantly more costly than TAP patients for restart episodes (+$4951, p<0.05) and augmentation episodes (+$2990, p<0.05). Conclusion: In a commercially-insured population, there are no significant differences in total post-treatment costs for AAPs patients relative to TAPs patients. Treating patients with schizophrenia with a mood stabilizer may lead to significantly higher cost.