OBJECTIVE: To investigate the association of antipsychotic polypharmacy in schizophrenia with cost of primary and secondary health service use. METHOD: Comparative analysis of health service cost for patients prescribed antipsychotic polypharmacy versus antipsychotic monotherapy. Resource utilisation and costs were described using central Danish registers for a 2 year period (2007-2008). We included patients attached to one of two Danish psychiatric referral centres in 1 January 2008 and/or 1 January 2009. Their prescribed treatment with either antipsychotic polypharmacy or monotherapy at the two cross-sectional dates was recorded and used as proxy of polypharmacy exposure during the preceding year. A multivariate generalised linear model was fitted with total costs of primary and secondary health service use as dependent variable, and antipsychotic polypharmacy, diagnosis, age, gender, disease duration, psychiatric inpatient admissions, and treatment site as covariates. RESULTS: The sample consisted of 736 outpatients with a diagnosis in the schizophrenia spectrum. Antipsychotic polypharmacy was associated with significantly higher total health service costs compared with monotherapy (2007: 25% higher costs; 2008: 17% higher costs) when adjusting for potential confounders and risk factors. A subgroup analysis suggested that the excessive costs associated with antipsychotic polypharmacy were partly accounted for by the functional level of the patients. CONCLUSION: The results demonstrate that antipsychotic co-prescribing is associated with increased use of health care services, even though no causal relations can be inferred from an observational study.