Medication alert systems have been implemented worldwide. The purpose of this study is evaluation of the medication alert systems from a clinical perspective. We surveyed physicians with regard to their reactions to the medication alerts. We collected the revised prescription information and assessed risk avoidance in all cases. The system reviewed 51,006 prescriptions and produced 16,718 physician alerts related to 13,823 prescriptions over the course of 1 month. We identified 45 prescriptions that were revised following the alert and four cases in which patient treatment may have been discontinued or adverse drug events (ADEs) may have occurred if the alerts had not been issued. We demonstrated that the system prevented these potential medication errors. This study adopted a clinical perspective and demonstrated that a real-time alert system can contribute to prevention of ADEs.