The Military Health System (MHS) and the Veterans Health Administration (VHA) have been among the nation's leaders in health information technology (IT), including the development of health IT systems and electronic health records that summarize patients' care from multiple providers. Health IT interoperability within MHS and across MHS partners, including VHA, is one of ten goals in the current MHS Strategic Plan. As a step toward achieving improved interoperability, the MHS is seeking to develop a research roadmap to better coordinate health IT research efforts, address IT capability gaps, and reduce programmatic risk for its enterprise projects. This report contributes to that effort by identifying gaps in research, policy, and practice involving patient privacy, consent, and identity management that need to be addressed to bring about improved quality and efficiency of care through health information exchange. Major challenges include (1) designing a meaningful patient consent procedure, (2) recording patients' consent preferences and designing procedures to implement restrictions on disclosures of protected health information, and (3) advancing knowledge regarding the best technical approaches to performing patient identity matches and how best to monitor results over time. Using a sociotechnical framework, this report suggests steps for overcoming these challenges and topics for future research.