OBJECTIVE In eHealth development there is an increasing focus on user participation inspired by the information systems field of practice and research. There are, however, many other challenges in developing information systems that fit healthcare practices. One of these is the challenge of cooperation and communication in development projects that are initiated and managed by clinicians e.g. cooperating with IT professionals in 'bottom up' health informatics projects that have been initiated and are managed by healthcare professional project managers. METHODS The analysis and results are drawn from a qualitative case study on a systems development project that was managed by a local, non-technical, healthcare professional and the complex blend and interactions with the IT professionals in the phases of ideas, design, development, implementation, maintenance and distribution. RESULTS We analyze the challenges of cooperation and communication using perspectives from information systems research and the concepts of 'language-games' and 'shared design spaces', and thereby exploring the boundaries between the different communication, practice and culture of the IT professionals and the healthcare professionals. CONCLUSIONS There is a need to (a) develop a better understanding of the development process from the point of view of the 'user' and (b) tools for making technical knowledge explicit in the development process. Cooperative and communicative methods are needed that support and develop the shared design spaces between IT professionals and the clinical context in order to strengthen small-scale health information systems projects.