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Recently, there has been an emphasis on collecting large datasets in the field of sports medicine. While there have been great advances in areas of sport performance and sport epidemiology, there have been fewer efforts dedicated to understanding the effectiveness and impact of athletic healthcare, including injury prevention programs and rehabilitation interventions provided at the point-of-care. In 2009, the Athletic Training Practice-Based Research Network (AT-PBRN) was launched to address this need, with the mission of improving the quality of care provided by athletic trainers. Unlike other research efforts in sports and medicine, such as sport epidemiology, there are fewer methodological best practices specifically related to clinical data in athletic healthcare. As a result, the AT-PBRN has encountered several methodological challenges during its tenure and has established guidelines based on various sources within the fields of sports and medicine to address these challenges. Therefore, the purpose of this perspective is to identify the challenges and describe strategies to address these challenges related to characterizing athletic healthcare using a large database. Specifically, challenges related to data entry (data quality and reliability) and data extraction and processing (data variability and missing data) will be discussed. Sharing challenges and perspectives on solutions for collecting and reporting on athletic healthcare data may facilitate a greater consistency in the approach used to collect, analyze, and report on clinical data in athletic healthcare, with the goal of improving patient outcomes and the quality of care provided by athletic trainers.