Electronic health records (EHRs) offer significant advantages over paper charts, such as ease of portability, facilitated communication, and a decreased risk of medical errors; however, important ethical concerns related to patient confidentiality remain. Although legal protections have been implemented, in practice, EHRs may be still prone to breaches that threaten patient privacy. Potential safeguards are essential, and have been implemented especially in sensitive areas such as mental illness, substance abuse, and sexual health. Features of one institutional model are described that may illustrate the efforts to both ensure adequate transparency and ensure patient confidentiality. Trust and the therapeutic alliance are critical to the provider-patient relationship and quality healthcare services. All of the benefits of an EHR are only possible if patients retain confidence in the security and accuracy of their medical records.