Background: It often remains unclear to investigators how their research contributes to the work of the commissioner. We initiated the 'Risk Model' case study to gain insight into how a Dutch National Institute for Public Health and the Environment (RIVM) project and its knowledge products contribute to the commissioner's work, the commissioner being the Health Care Inspectorate. We aimed to identify the alignment efforts that influenced the research project contributions. Based on the literature, we expected interaction between investigators and key users to be the most determining factor for the contributions of a research project.Methods: In this qualitative case study, we analyzed the alignment efforts and contributions in the Risk Model project by means of document analysis and interviews according to the evaluation method Contribution Mapping. Furthermore, a map of the research process was drafted and a feedback session was organized. After the feedback session with stakeholders discussing the findings, we completed the case study report.Results: Both organizations had divergent views on the ownership of the research product and the relationship between RIVM and the Inspectorate, which resulted in different expectations. The RIVM considered the use of the risk models to be problematic, but the inspectors had a positive opinion about its contributions. Investigators, inspectors, and managers were not aware of these remarkably different perceptions. In this research project, we identified six relevant categories of both horizontal alignment efforts (between investigators and key users) as well as vertical alignment efforts (within own organization) that influenced the contributions to the Inspectorate's work.Conclusions: Relevant alignment efforts influencing the contributions of the project became manifest at three levels: the first level directly relates to the project, the second to the organizational environment, and the third to the formal and historical relationship between the organizations. Both external and internal alignments influence the contributions of a research project. Based on the findings, we recommend that research institutes invest in a reflective attitude towards the social aspects of research projects at all levels of the organization and develop alignment strategies to enhance the contributions of research. © 2014 Hegger et al.; licensee BioMed Central Ltd.