OBJECTIVES: The aim of this study was to evaluate the probability of metabolic syndrome caused by atypical antipsychotics after long term therapy and the cost of pharmacist interventions to improve these metabolic adverse effects. METHODS: A total of 431 adults prescribed atypical antipsychotics therapy from 2002 to 2007 were retrieved from the claim database. The primary outcome measurement was the probability of metabolic syndrome caused by atypical antipsychotics after long term therapy. The secondary outcome was to evaluate the cost of pharmacist intervention. Pharmacist consultation clinic for measuring their waist, buttocks, pharmaceutical education and body weight management. Computerized physician order entry alerting system for abnormal metabolic chemical variables  remind physician to attend patients abnormal laboratory data and adjust the treatment regimen. RESULTS: The primary outcomes showed that the total rate of metabolic syndrome induced by atypical antipsychotics were 16% (48/298). The secondary outcome, the abnormal BMI value of 50 patients,who received pharmacist consultation services, decreased from 52% to 41%. After establishment of computerized physician order entry alerting system, the possibility of patients’ abnormal biochemical values induced by atypical antipsychotics decreased from 4.28% (33/771) to 1.23% (8/651). The clinical effectiveness of this research included the occurrence of dyslipidaemia and disorders of glucose homeostasis associated with cardiovascular disease. The total direct medical cost saved for this pharmaceutical care was approximately NT 1,428,250 during this study period. CONCLUSIONS: All patients receiving atypical antipsychotic agents associated with metabolic adverse events should be routinely monitored on weight gain, abnormal blood glucose and lipid levels. The effective communication and collaboration with mental health care and pharmaceutical care services is an effective model for caring patients with mental disease.