Access to multi-site clinical data regarding treatment and outcomes of HIV-infected patients in routine care is required to support clinical research to improve the treatment of HIV. As part of the NIAID-funded CFAR Network of Integrated Clinical Systems (CNICS), we have developed a relational XML Schema to extend the existing observational research repository and to integrate real-time clinical information from electronic medical records (EMRs) at six Centers for AIDS Research (CFAR) into the repository. The schema will aid the expansion of the research repository beyond the initial sites, and the development process may facilitate the use of multi-site repositories to study other chronic diseases.