As vice-president of the James S. McDonnell Foundation (JSMF), I wish to clarify our position on the recovery of indirect research costs, which include overheads such as administration and building-maintenance costs (Nature 476, 385; 2011). You are correct in that the JSMF does not allow applicant institutions to include indirect costs as a component of budget requests; however, this should not be branded as a 'refusal' to fund indirect costs.

The JSMF, like many private foundations, considers it inappropriate for institutions to request indirect costs from private funders. In the United States, recovery of indirect costs by universities is negotiated with federal funding agencies because most US-funded research is done on university campuses.

It is unfortunate that a misunderstanding over the history and reasons for recovering indirect costs continues to strain relations between universities and private funders. A core mission of universities and education is the creation of new knowledge through research and scholarship. Grants from private funders such as the JSMF are helping universities to realize these goals; contrary to common belief, foundation grants are budget-relieving, not budget-additive. Providing for indirect costs would be incompatible with this traditional relationship.