Budgets do not only pay the costs of activities. They also reveal the ambitions and limitations of an organization. The opportunities presented in a budget are also bounded by the structural elements used by that institution: how costs and revenues are organized, how overhead is calculated and apportioned, and how assets and investments are calculated and utilized, among others. In the higher education sector in the US, there are many common budgeting elements but also several important areas of differentiation. This issue brief provides a summary of two important elements of academic budgeting at large research universities and for externally funded research: budget models and indirect costs.