Reducing new HIV infections in the United States requires allocating public resources to interventions that will have the greatest impact on reducing the number of new infections. We report on the organizational experience of a federal agency's efforts to align its HIV prevention resources to reflect the specific priorities of a five-year strategic plan that has as its goal a fifty percent reduction in the number of annual HIV infections nationwide. Structural and other impediments encountered during the alignment process, and the steps taken to minimize their impact are described, adding to the empirical data base of strategic planning experiences in the public sector.