The assessment and prioritisation of research activity are essential components of any Science, Technology and Industry System. Data on researchers' perspectives in this respect are scarce. The objective of this paper was to describe Spanish scientists' point of view on the current evaluation system in Spain and how they believe this system should be functionally structured.From the sampling frame formed by established Spanish scientists, listed in the databases of CSIC and FIS (Institute of Health Carlos III), clinical, biomedical-non clinical, and physics and chemical researchers were randomly selected. Two hundred and eleven interviews were carried out by means of a computer-assisted telephone interviewing system.Researchers expressed their acknowledgement of progress in the Spanish research field but made their wish clear to progress towards better scientific scenarios. In their assessment, they gave a score of 5.4 to scientific policy, as opposed to 9.4 when speaking about the goals, reflecting the desire for a better policy definition, with clear objectives, stable strategies and better coordination of R&D activities (the current coordination received a score of 3.9, while the desirable coordination was valued as high as 9.2). There was certain agreement regarding the need for a prioritisation criteria which preserves some degree of creativity by researchers. They also stated that they would like to see an independent research structure with social prestige and influence.The interviewed researchers believe that the evaluation of scientific activities is fundamental in formulating a sound scientific policy. Prioritisation should arise from appropriate evaluation. Strategies properly coordinated among all the stakeholders (including the private sector) should be fostered. Budget sufficiency, stability, and better organization of independent researchers should be the backbone of any strategy tailored to increase their capacity to influence future scientific policies.