It is the purpose of this article to discuss the development and application of a logic model in the context of a large scientific research program within the Commonwealth Scientific and Industrial Research Organisation (CSIRO). CSIRO is Australia's national science agency and is a publicly funded part of Australia's innovation system. It conducts mission-driven scientific research focussed on delivering results with relevance and impact for Australia, where impact is defined and measured in economic, environmental and social terms at the national level. The Australian Government has recently signalled an increasing emphasis on performance assessment and evaluation, which in the CSIRO context implies an increasing emphasis on ensuring and demonstrating the impact of its research programs. CSIRO continues to develop and improve its approaches to impact planning and evaluation, including conducting a trial of a program logic approach in the CSIRO Preventative Health National Research Flagship. During the trial, improvements were observed in clarity of the research goals and path to impact, as well as in alignment of science and support function activities with national challenge goals. Further benefits were observed in terms of communication of the goals and expected impact of CSIRO's research programs both within CSIRO and externally. The key lesson learned was that significant value was achieved through the process itself, as well as the outcome. Recommendations based on the CSIRO trial may be of interest to managers of scientific research considering developing similar logic models for their research projects. The CSIRO experience has shown that there are significant benefits to be gained, especially if the project participants have a major role in the process of developing the logic model.