OBJECTIVES: To determine patterns in the prescriptions of antipsychotics in patients with mood disorders.   To investigate adverse effects of antipsychotics in patients with mood disorders and their relationship to other prescription drugs.   METHODS: The MarketScan database, for year 2000, containing information on outpatient doctor visits and consumption of prescription drugs on millions of Americans with health care coverage was used.  Patients with at least a mood disorder were identified by ICD9 codes.  Their prescription drug record for this year was also identified.  This was populated with drugs names by NDC codes tables from the FDA website.  Antipsychotic drug use was categorized as first generation or second generation and logistic regression was used to determine odds ration controlling on demographics.  Furthermore, patients were classified as having a metabolic disorder, such as hyperglycemia or diabetes, and odds ratios were computed controlling for the generation of the antipsychotic.  The data were also analyzed using data mining techniques such as cluster analysis and link analysis.   RESULTS: Antipsychotics were highly used in the treatment of mood disorders.  Second generation antipsychotics were prescribed almost two times more often than first generation antipsychotics.  The odds of having a metabolic disorder are almost 50% higher for patients using second generation antipsychotics than for patients using first generation antipsychotics.  Cluster analysis shows that metabolic disorders and other chronic diseases are rather common among patients with mood disorders. Link analysis shows that the use of second generation antipsychotics is strongly connected to the use of antidepressants.   CONCLUSIONS: These findings suggest that people taking second generation antipsychotics should be closely monitor for the development of metabolic disorders.  More efforts should be made to investigate the association between chronic diseases and mood disorders.