Background It is no exaggeration to say that, in Japan, the primary treatment approach for patients with schizophrenia continues to be high-dose antipsychotic polypharmacy. However, the supporting evidence for the efficacy of antipsychotic polypharmacy is insufficient. In fact, antipsychotic polypharmacy is more likely to cause side effects, increase mortality, and decrease treatment adherence. Further, on average, mortality in patients with schizophrenia is 20 years earlier than in people without schizophrenia, and the gap is widening. One potential explanation for the increased mortality rates observed in patients with schizophrenia is that they are at higher risk for metabolic syndrome, indicated by increased rates of obesity, hypertension, dyslipidemia, and diabetes. Results Therefore, we recruited 7,655 outpatients and 15,461 inpatients with schizophrenia from the facilities of the Japan Psychiatric Hospitals Association and conducted a large-scale investigation of the prevalence of obesity, hypertension, dyslipidemia, and diabetes mellitus using a questionnaire. We also examined the relationship between antipsychotic polypharmacy on the parameters that regulate each lifestyle-related disease. As a result of examining the relationship between parameters that regulate each lifestyle-related disease and antipsychotic polypharmacy, we found that the more antipsychotics a patient was on, the higher their values for body mass index, diastolic blood pressure, low-density lipoprotein cholesterol and fasting blood glucose were. Conclusion The present study demonstrates that antipsychotic polypharmacy may actually exacerbate obesity, hypertension, dyslipidemia and diabetes. Therefore, it may be better to utilize alternative treatment strategies other than antipsychotic polypharmacy in order to avoid these metabolic side effects.