The resources for health technology assessment fall short of that needed to evaluate all health technologies. Therefore, priorities have to be set. In The Netherlands, the Health Care Insurance Board tried to address this issue by developing a more explicit priority setting procedure for the Fund for Investigative Medicine, which is the most important health technology assessment programme in The Netherlands. The procedure provides one of the first examples of the application of theoretical principles for priority setting. The aim is to select those health technologies for assessment that are most relevant for policy-making. To determine the policy relevance of research proposals, different procedures for categorising, scoring, and weighting policy criteria were defined, and different classification strategies were explored. Our first experiences using the priority setting procedure are described by means of an example on low back pain. Subsequently, the procedure has been applied to research proposals submitted to the Fund for Investigative Medicine in 1998 to illustrate how decisions on the funding of health technology assessments can be guided. The results show a different rating of research proposals into one of three predefined categories of policy relevance, high, intermediate and low, implying that decisions about funding can heavily dependent on the selected procedure. Therefore, it seems to be important that the selected procedure reflects the viewpoint of the organisation wishing to set priorities. The different ratings of the research proposals using a more explicit procedure suggest that there may be scope for further development and application of the procedure.