Pandemic influenza is an imminent threat, with the April/May 2009 A(H1N1) outbreak as a testament to the potential for rapid transmission and spread of a novel influenza strain. Research has shown that there are great disparities in state pandemic planning; however, little work has been done to assess how health department structure impacts pandemic preparedness. The purpose of this article was to examine the impact of state health department structure on state pandemic influenza plan integration of federal recommendations. The study consisted of a cross-sectional analysis of 41 states and found that structural and strategy-making variables have the greatest impact on pandemic plan inclusion of federal recommendations. Strong, multilayered health department hierarchies and the tenure of senior staff are negatively associated with preparedness, whereas professionalization is positively associated with pandemic plan comprehensiveness. State health departments can take minimally invasive steps to increase their effectiveness in pandemic preparedness by reducing layers of bureaucracy and increasing training for staff.