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Clinical and applied health research is led by academics and often conducted in the National Health Service (NHS). Researchers work with Research Support Offices in both Universities and the NHS. The 2006 government health research strategy, Best Research for Best Health heralded dramatic changes for both the funding of, and support for, clinical and applied health research in England with the creation of new, quality driven, competitive funding streams and a new infrastructure to support research and researchers. One of the results of these changes was to drive NHS and University Research Support Offices closer together, with some institutions forming close partnerships, including joint offices to deliver support for clinical and applied health research. Little is known about the models of partnership working between the universities and the NHS and the factors that drove the decisions to create partnership Research Support Offices. Therefore it is important to map current arrangements and describe the factors that contribute to those arrangements. Firstly a survey of University Research Support Offices based in universities with a medical school was undertaken to provide a snapshot of the structures and functions of those Research Support Offices. Then semistructured interviews were undertaken with a sample of staff working in joint NHS/University and separate NHS and University Research Support Offices to gain a deeper understanding of why the Research Support Offices were structured and functioned in the ways that they did. The main findings from this work were: there are no common structures, functions, or systems and few common processes in place to support clinical and applied health researchers across England; advice and help for navigating the complex regulatory environment currently underpinning clinical and applied health research in England is fragmented; three models of working between NHS and university Research Support Offices were identified; joint offices, collaborative offices and separate offices. The drivers for joint working between NHS and University Research Support Offices are compelling. However, the barriers to working closely can be immense if not carefully considered. Those contemplating working in partnership need to ensure that they understand what the partnership aims to deliver and all partners need to commit to a shared vision. In addition, practical issues such as the systems to be used, the physical location of staff and employment issues need to be addressed in advance before meaningful joint working can occur.