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During the last 20 years, science policy-making has taken to evaluation as an instrument for assessing research projects, programmes and even entire research institutes or faculties. This article examines key elements of the evaluation systems in the United Kingdom (Research Assessment Exercise), the Netherlands (Standard Evaluation Protocol) and Germany (Leibniz Association’s Evaluation Procedure) and the extent to which evaluations serve as an instrument of organizational development for the scientific bodies being evaluated. Evaluations are often mistrusted – particularly in Germany’s public discourse – as a Trojan horse of policy-making infiltrating the science system. However, our findings demonstrate that peer-review based evaluations can be an authoritative source of validation employed by scientific institutes to develop or optimize institutional strategies. Against this backdrop, we conclude with recommendations of how institutional evaluations may be further developed and how processes of organizational transformation can be supported in the research landscape. [ABSTRACT FROM PUBLISHER]