This article looks at American foreign policy towards Kosovo and East Timor in 1999 using the extant literature, internal Administration documents, as well as elite interviews. I then test these cases against a structured focused comparison of two competing hypotheses. The first is realism. Secondly, I develop a hypothesis of institutional agenda setting, based on constructivism and neo-liberal institutionalism. I contend that the best explanation for both cases lies in the second hypothesis. Institutional identity shapes state preferences, not only in decisions to intervene but in shaping the size and scope of the mission. Institutions matter in complex human emergencies.