Since 1975 more than twenty European Community Agencies have been established, and there is considerable variation in terms of the functions these agencies are set up to perform. Drawing on new institutionalist theories and public management literature, this paper investigates whether or not there are different rationales behind the establishment of regulatory agencies on the one hand and advisory agencies on the other. Particular focus is placed on the examples of the regulatory agencies EMEA and EASA, and the advisory agencies Cedefop and FRONTEX). The paper argues that rational choice institutionalism holds better explanatory value when commercial interests were key driving forces behind agency creation as appears to be case with regulatory agencies. The advisory agencies are better explained through analysis of the political climate at the time of agency establishment.