Since the migration from paper health records to electronic health records (EHR) began, there have been many confidentiality problems which have arisen and been addressed; however, the implementation of adolescent confidentiality in the EHR has yet to be successfully executed. We sought to identify issues and best practices during the conversion of health records from paper to an electronic health record (EHR) in school-based wellness clinics because of an ongoing conversion project in the ChristianaCare, a private not-for-profit regional healthcare system in Delaware. This paper will explore the legal and societal challenges of adolescent medicine, how an EHR may augment these challenges, and the unique obstacles personally encountered during the implementation of an EHR in a school-based wellness clinic serving adolescent patients.