Sec. B — Run your own numbers

Indirect cost rate calculator: what's your recovery gap?

Two ways in. Start from your Form 990 — five figures off Part IX, the statement of functional expenses, plus, if any grant to an organization is $50,000 or more, a count and total worked out from Schedule I (domestic grants) and Schedule F (foreign) — or enter your rate figures directly if you already know your pools and base. Either way you get your modified total direct costs (MTDC), your rate-determination base, your actual indirect cost rate, and what you'd recover under the 15% de minimis rate vs. a negotiated rate, using the 2024 Uniform Guidance rules (15% de minimis; the first $50,000 of each subaward counts toward MTDC; unallowable-activity costs held in the rate base per § 200.413(e)).

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Program services — totalForm 990 Part IX, line 25, column (B). Same line on your audited statement of functional expenses.

Of that — grants & subawards to organizations, totalPart IX lines 1 (domestic) and 3 (foreign), column (B). Grants to individuals — line 2, and any foreign individuals in line 3 — are not subawards; enter their scholarship and participant-support part in A.3 instead.

How many of these subawards are $50,000 or more?Schedule I, Part II (domestic) and Schedule F, Part II (foreign) list each recipient over $5,000 with its grants summed, not each subaward — split out a recipient with several subawards. Blank or 0 if all are under $50,000. Only the first $50,000 of each subaward counts toward MTDC, once over its life.

Their combined totalOnly the subawards of $50,000 or more. A continuing subaward that used its first $50,000 in an earlier year: include its amount here but leave it out of the count, so it adds $0.

Of that — MTDC-excluded costs (often $0)Equipment and capital expenditures, rent, patient care, tuition remission, scholarships & fellowships, participant support (2 CFR 200.1). On Part IX, column (B): line 2 (scholarships, participant support) and the rent portion of line 16, occupancy. Depreciation (line 22) stays in.

Management & general — totalPart IX, line 25, column (C). This becomes your indirect cost pool.

Fundraising — totalPart IX, line 25, column (D). Never chargeable to an award, but § 200.413(e) keeps it in the base that computes your rate.

Modified total direct costs — MTDCProgram services less grants and exclusions, plus capped subawards (computed) —

Rate-determination baseMTDC + fundraising — 2 CFR 200.413(e) (computed) —

Your indirect cost rateManagement & general ÷ rate base (computed) —

Load an example 990

A.2 + A.3 exceed A.1. Grants and excluded costs are carved out of the program services column, so together they cannot be larger than it. Check that A.1 is the column (B) total.

Determination

De minimis (15% MTDC)

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Negotiated rate

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Left on the table

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Methodology & what MTDC includes

MTDC (modified total direct costs) follows 2 CFR 200.1 as revised in 2024: direct salaries and wages, applicable fringe benefits, materials and supplies, services, travel, and up to the first $50,000 of each subaward, regardless of the subaward's period of performance.

Excluded from MTDC: equipment, capital expenditures, charges for patient care, rental costs, tuition remission, scholarships and fellowships, participant support costs, and the portion of each subaward above $50,000.
Subawards in MTDC: your subaward total, less the combined total of the subawards of $50,000 or more, plus $50,000 for each one counted. Every subaward under $50,000 counts in full; each larger one adds exactly $50,000. The first $50,000 counts once over a subaward's life, so a continuing subaward that used it in an earlier year sits in the combined total but not the count, and adds nothing. One that used only part of its first $50,000 earlier can't be entered exactly here; a rate proposal works it subaward by subaward.
Rate-determination base: per 2 CFR 200.413(e), the direct costs of unallowable activities (fundraising, lobbying) remain in the base used to compute the rate even though they can never be charged to awards. Omitting them is a standard reviewer deficiency.
The "negotiated rate" column applies your computed rate to award-chargeable MTDC and assumes your awards permit indirect costs at the negotiated rate. With unallowable-activity costs entered, their share of overhead correctly remains with unrestricted funds. Some programs cap or restrict indirect recovery.
Federal share (C.1): the de minimis and negotiated rates are recovered on federal awards, so the dollar figures are scaled to the share of these direct costs charged to them. The rate itself is not scaled — it is computed across all of your activity, federal and non-federal alike.

What this is — and isn't

This is a planning estimate to size the decision between the de minimis election and a negotiated rate. It is not a rate proposal, an audit opinion, or accounting advice — your actual rate depends on allowability, allocability, and how your cost pools are built. That's the work we do; the free consultation is where it starts.