The terror attacks of September 11, 2001, posed a set of security challenges for the nation’s cities that the increasingly decentralized federal system was poorly prepared to meet. Although it was generally agreed that domestic security required a close intergovernmental partnership, strong national leadership and support were lacking in creating and guiding this partnership. To make matters more difficult, political considerations in Congress generally trumped the assessment of security risks in the distribution of federal fiscal aid. This article explores the strains in the intergovernmental homeland security partnership, their causes, and efforts to adapt and reform. Despite some progress toward a more rational public administration of homeland security, the partnership still reflects the deficiencies of imperfect federalism.