Practitioners in federally-assisted substance use disorder (SUD) treatment programs are faced with increasingly complex decisions when addressing patient confidentiality issues. Recent policy changes, intended to make treatment more available and accessible, are having an impact on delivery of SUD treatment in the United States. The addition of electronic health records provides opportunity for more rapid and comprehensive communication between patients' primary and SUD care providers while promoting a collaborative care environment. This shift toward collaborative care is complicated by the special protections that SUD documentation receives in SUD treatment programs, which vary depending on what care is provided and the setting where the patient is treated. This article explores the special protections for substance abuse documentation, discrepancies in treatment documentation, ways to deal with these issues in clinical practice, and the need for more knowledge about how to harmonize treatment in the SUD and primary care systems.