We have a customer who deposited $13,000 into a joint account owned by USDA and himself. How should the CTR be filed? Individual only because USDA is exempt or both?

Call the FinCEN helpline.

I also assume they had permission to make the deposit??

(b) Deposits by borrowers. Funds in the form of cash, check, or money order may be deposited in the supervised bank account by the borrower if authorized by Rural Development provided the financial institution has agreed that when a deposit is made to the account by other than Rural Development personnel, the financial institution will promptly deliver or mail a copy of the deposit slip to the Rural Development Servicing Office.

(1) A loan or grant check drawn on the U.S. Treasury may be deposited in a supervised bank account by a borrower, provided the following endorsement is used and is inserted thereon prior to delivery to the borrower for signature:

"For deposit only in my supervised bank account
in the (name of financial institution and address when
necessary for identification) pursuant to Deposit Agreement
dated ________________________________."

(2) Funds other than loan or grant funds may be deposited by the borrower in those exceptional instances where an agreement is reached between the Servicing Official and the borrower, whereby the borrower will make deposits of income from any source directly into the supervised bank account. In such instances the borrower will be instructed to prepare the deposit slip in the manner described in
§ 1902.9(a)(5) of this subpart.