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Introduction: Prevalence of menstrual dysfunction (MD) in high school athletes ranges from 7% to 54%. Early recognition and intervention are crucial to prevent future consequences. The purpose of this Quality Improvement project was to optimize the institution’s Epic Best Practice Advisory (BPA) screening tool and synthesize new patient questionnaires to diagnose MD in athletes greater than 12 years of age presenting to a pediatric sports medicine clinic. Methods: Using Quality Improvement methodology, we evaluated clinic flow, the Epic BPA tool, and actions by the physician following the appropriate triggering of the BPA. Diagnoses targeted were primary amenorrhea, oligomenorrhea, or irregular menstruation unspecified. Areas for intervention were global staff education, patient education, and provider alert fatigue. Our team implemented interventions using monthly Plan-Do-Study-Act cycles to address our key drivers. Proper implementation of questionnaire data and restructuring of the Epic BPA promoted identification and diagnosis of MD. The clinician discussed the diagnosis with the patient and family and provided an educational handout on MD. Results: The rate of appropriate diagnosis of MD in athletes greater than 12 years of age seen at a pediatric sports medicine clinic increased from a baseline of 2.1% to 30% over ten months. Identification of three key drivers ultimately drove the success and achievement of our aim. Conclusions: Using Quality Improvement methodology, we optimized the EPIC BPA and subsequently increased the rate of appropriate diagnosis of MD. Identification of the proper diagnosis improves our patient education. Ultimately, this project provided the framework for applicable discussion, interventions, and work-up for at-risk athletes.