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If a 501(c)(3) medical clinic for the under- and uninsured charges patients fees for services that don’t cover the total costs of operation and raises the remainder of the budget from charitable contributions, what can be the ratio of fees to contributions? 

The ratio can be whatever you want it to be, or are able to make it.

The IRS does not care about the ratio of fees to contribution.  It cares about the ratio of public support to total support to determine whether you have a sufficiently broad-based source of income to qualify as a publicly supported charity.  If not, you will be classified as a private foundation.

It makes very little difference whether you are 100% fees, 100% contributions, or somewhere in between. The way you calculate public support will differ depending on whether you are predominately fee based, or significantly gift based, but so long as you have a broad base of payors/donors you should ultimately qualify as a public charity.  The IRS now provides that the calculation will be based on a 5-year moving average, instead of a 4-year average as in the past. But the basic rules for categorizing support—and applying the limitations on the amount that qualifies as public support—have not changed. Those rules are spelled out in our Ready Reference Page:  “Calculating Public Support.”