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Background: Serotonin syndrome is a life-threatening disease if not appropriately treated. This study aimed to investigate the prescription status of contraindicated drug combinations that cause serotonin syndrome and identify the related factors. Methods: A cross-sectional study was conducted using nationwide claims data. Adult patients taking serotonergic drugs with Parkinson’s disease or mental disorders were selected. Based on international medical databases (MDBs) and the Korean Drug Utilization Review (DUR), the status of prescribing contraindicated drug combinations that induce serotonin syndrome, the related factors, and the difference between international MDBs and the Korean DUR were analyzed. Results: Of the 49,773 study subjects, 163 (0.3%) were prescribed contraindicated serotonergic drug combinations based on international MDBs, and among them, only 105 (64.4%) were contraindicated by the Korean DUR. Positive influencing factors for prescribing contraindicated drug combinations include patient age between 65 and 74 and physician’s specialties (neurologists, and orthopedists). Negative influencing factors were physician’s specialty (internists) and medical institution (primary institutions). Conclusion: Despite the implementation of DUR, 3 out of 1,000 study subjects received contraindicated drug combinations that caused serotonin syndrome. Hence, it is necessary to comply with the DUR and improve it in accordance with international MDBs.