Customer comes in to make a loan payment with $15,000 cash to pay off loan balance $14,950. He only has $100's The teller gives him $50 back, but records it as 15,000 cash in and $50 cash out. This is one transaction to make a loan payment. What's the CTR amount to be reported? I say $14,950 "In" If it is supposed to be $15000 in, what's the difference if the he got change for one of the 100's, and gave the teller the 14,950? It's the same thing. Auditor says otherwise. What am I missing?

$14,950 loan payment + $50 currency exchange = $15,000

Agree. The teller received $15000 and paid out $50, whether that's the way it is recorded in your cash account or not. So you report the receipt of $15000 as Randy has said above.

If the customer came in with $14,900 in $100s and two $50 bills and asked for the payoff amount ($14,950) before handing over cash, and only $14,950 crossed the counter, only the loan payoff of that amount would be reported.