This article uses the 2009 H1N1 influenza vaccination program experience to introduce a cost analysis approach that may be relevant for planning mass prophylaxis operations, such as vaccination clinics at public health centers, work sites, schools, or pharmacy-based clinics. These costs are important for planning mass influenza vaccination activities and are relevant for all public health emergency preparedness scenarios requiring countermeasure dispensing. We demonstrate how costs vary depending on accounting perspective, staffing composition, and other factors. We also describe a mass vaccination clinic budgeting tool that clinic managers may use to estimate clinic costs and to examine how costs vary depending on the availability of volunteers or donated supplies and on the number of patients vaccinated per hour. Results from pilot tests with school-based H1N1 influenza vaccination clinic managers are described. The tool can also contribute to planning efforts for universal seasonal influenza vaccination
