OBJECTIVES: To assess the relationship between newly initiated atypical antipsychotic (AA) use and subsequent diagnoses for the metabolic disorders (MD) of hyperlipidemia, diabetes, and obesity. METHODS: Enrollees in the South Carolina Medicaid program were included if they initiated AA therapy in 2003 or 2004 (index date), did not have a MD diagnosis in the 12 months prior to the index date, used only a single AA drug for the 12 months prior to and following the index date (follow-up), and were continuously eligible during follow-up. A comparison group with the same inclusion criteria was selected except this group did not have a MD during follow-up. Multivariate logistic regression was used for analysis with each of the three MDs as dependent variables. Independent variables included age, race, gender, and AA used with clozapine as the comparator. RESULTS: A total of 19,388 patients were identified (1,788 with a MD and 17,600 without MD). The study population was 46.7% male, 52.1% white, and had an average age of 42.7 (SD 24.2). In patients diagnosed with diabetes, olanzapine (OR = 1.59, 95% CI = 1.22-2.08, p = .001) and risperidone (OR = 1.47, CI = 1.12-1.92, p = .005) had significantly higher diagnosis rates. Patients taking risperidone (OR = 1.70, 95% CI = 1.15-2.53, p = .001) had a significantly higher rate of hyperlipidemia. Patients diagnosed with obesity had a significantly higher rate of diagnosis if they used olanzapine (OR = 1.85, 95% CI = 1.11-3.10, p = .020) or risperidone (OR = 1.92, 95% CI = 1.15-3.20, p = .012). CONCLUSION: Findings of this Medicaid-based study indicate that higher rates of diabetes, hyperlipidemia, and obesity are associated with use of certain atypical antipsychotics. Additional research is needed to confirm and elaborate the specifics of these metabolic disorders associated with atypical antipsychotic use.