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Research is more and more split up into scientific disciplines; this may lead to difficulties in associating different branches of specialized knowledge in projects of public usefulness, as innovation processes. The object of this paper is to discuss scientific evaluation of interdisciplinary projects in an innovation context. The development of creative activities is often handicapped by faulty evaluation, while interdisciplinary creativity is largely supported by decision-makers, it is less so by peers, who are often involved in a form of conservatism of paradigms, associated with mono-disciplines. The robustness of traditionally used indicators will be discussed in regard with perceived reputation of researchers involved in interdisciplinary projects. Most of the methodologies for assessing research performance today are largely based on quantitative evaluation using bibliometric indicators, which is not adequate to evaluate interdisciplinary research. In this paper, proposals are made, aiming at developing better methods to assess reputation in the science of complexity, associating integration of scientific fields and leading to innovation. This kind of proposal can lead to changes in the culture of evaluators (and of some researchers) since they will have to take into account a new notion of excellence, associated with a more applied vision, including innovation and the usefulness to Society.

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