Do you pay the fees out of the self directed IRA account?
I pay the fees as they are billed to me. The account is only real estate parcels. I get the bill for the taxes then I send the money to the IRA company, since it has to be paid through them to be deductible. But I dont under stand why the fees that I pay them for maintenance of the account are not on a 1099.
The IRA maintenance fees are a deductible as a miscellaneous 2% item on Sch A. They are not part of the IRA deduction that goes on the front of the Form 1040.
If you look at your Sch A, the section you are looking at is the bottom one. To claim miscellaneous deductions you must first subtract 2% of your adjusted gross income. If the amount of the expense exceeds that number then you can take the balance.
In addition to IRA maintenance fees employee business expenses, tax preparation fees, legal fees related to income, investment expenses also go into this number.