We found out that our son's university, which declared itself a non-profit, charged excess tuition fees, using those for its endowment. Is the excess deductible?

[mgfrobozz]

Only  a tiny fraction of what we paid was from grants. The Feds required the university to use the contribution to the endowment to pay for tuition for incoming students, instead of returning it to us.

[Hal_Al]

Q.  Is the excess deductible?

A. No. At least, no more than usual.

That is,  the total tuition you paid, including the "excess" can be counted in calculating your tuition credit or deduction.