NIH and NSF Indirect Costs: What They Actually Mean for Researcher Compensation

A widely misunderstood line item

Federal research grants from agencies like the NIH and NSF are typically awarded as two components: direct costs, which fund the actual research — personnel salaries charged to the grant, equipment, supplies, and other project-specific expenses — and indirect costs (formally "Facilities and Administrative," or F&A, costs), which reimburse the institution for overhead supporting the research broadly: building operations and maintenance, utilities, library resources, sponsored research administration, and similar shared infrastructure that is not attributable to any single grant.

Indirect cost rates are negotiated, not fixed

Each institution negotiates its own indirect cost rate with the federal government (typically through a cognizant agency), and rates vary substantially by institution type — research universities commonly negotiate rates that, expressed as a percentage of modified total direct costs, run considerably higher than many researchers assume, since the rate is calculated against a specific direct-cost base with its own exclusions (equipment and tuition remission are commonly excluded from the base, for example), not against the grant's full award amount. Because rates and calculation methodologies are institution-specific and subject to periodic renegotiation and policy changes at the federal level, researchers should treat any indirect cost percentage they hear cited elsewhere as illustrative rather than universal, and check their own institution's current negotiated rate agreement directly.

To illustrate the mechanics: if a grant's modified total direct costs total $200,000 and the institution's negotiated F&A rate is 55 percent, the award typically includes an additional $110,000 in indirect cost reimbursement paid to the institution — bringing the total award to $310,000 — but that $110,000 is never available to the researcher's direct budget for personnel, equipment, or supplies, regardless of the direct-cost total. Researchers who see only the total award figure sometimes mistakenly believe a much larger direct-cost budget is available to them than the grant's actual direct-cost line permits.

Why indirect costs are not "lost" money from a researcher's perspective

A common misconception is that indirect costs represent money "taken away" from a researcher's project that could otherwise have funded more direct research or higher personnel pay. In reality, indirect cost reimbursement funds the institutional infrastructure — laboratory space, safety compliance, grant administration support, and shared research computing, among other things — that direct research activity depends on and that direct costs are generally not allowed to fund even if a researcher wanted to allocate a grant that way. Direct cost budgets, not indirect cost rates, are what determine how much a researcher can actually charge toward their own salary or their team's personnel costs on a given grant.

How this connects to researcher compensation specifically

A researcher's salary charged to a grant is a direct cost, budgeted and justified separately from the indirect cost calculation, and subject to its own institutional policies — including, at many institutions, salary cap policies that limit the portion of a researcher's institutional base salary that can be charged to a federal grant (the NIH, for example, has historically applied a salary cap tied to a specific federal pay scale, independent of the researcher's actual institutional salary, meaning high earners may need to have a portion of their effort-based salary covered by non-grant institutional funds). Researchers on soft-money or partial soft-money appointments (see our companion piece on grant-funded salary planning) should understand their institution's specific salary cap and cost-sharing policies, since these directly determine how much of their compensation a given grant award can actually cover.

A researcher paid partly on a salary-capped federal grant and partly through institutional funds should confirm, specifically, how the gap between their actual institutional salary and the applicable federal cap is covered — whether through general institutional funds, another grant, or a required cost-sharing commitment from the department — since this gap does not disappear simply because the grant budget does not show it explicitly.

A practical framework for understanding your own grants

• Look up your institution's current negotiated F&A rate agreement rather than assuming a generic percentage.
• Understand which cost categories are excluded from the modified total direct cost base used to calculate indirect costs on your specific grants.
• Confirm whether any applicable salary cap policy limits how much of your compensation a given federal award can cover, and how any gap is funded.
• Distinguish, in any grant budget you review, between what indirect costs fund institutionally and what your direct cost budget actually controls for your own team.
• Ask your sponsored programs office to walk through a specific grant budget line by line if the direct-versus-indirect split is ever unclear — this is a routine request they field often, not an imposition.

The takeaway

Indirect costs are institutional infrastructure reimbursement, not money diverted from a researcher's direct compensation or research budget — but the direct-cost side of a grant, including salary caps and cost-sharing policies, has very real and specific effects on what a given award can pay toward a researcher's own salary. Understanding both pieces separately clears up one of the most persistent points of confusion in academic research funding.