Depending on the code in box 7 on the 1099-R and if the IRA/SEP/SIMPLE box is checked, the box 1 amount should appear on your 2017 1040 form line 15a or 16a (lines 11a or 12a on a 1040A form).
Even if box 2a is zero you are still required to report the 1099-R on your tax return or the IRS can assume that you did not complete the transaction that made it not taxable.
There can be some situations where such as rolling what would otherwise be non-taxable into the wrong type of account that makes it taxable.
box 2 is blank or $0 if the trustee has not determined its taxability . the box taxability not determined should be checked. why is it left blank or $0? the trustee doesn't now if you have made any nondeductible IRA contributions. if you did not all the amount withdrawn would be taxable. this is a frequent problem I've seen on many 1099-R.
It would appear that the 1099-R is not correct. If box 2b (not determined) is checked then box 2a must be BLANK, not zero. Check again - an empty box 2a is NOT the same as zero - it it the opposite in most cases and means the that box 1 is probably the taxable amount unless you had after-tax basis in the account.
Code 3 means disability and the taxable amount (probably box 1) should be included as wages if you are under retirement age or taxed as a pension of over retirement age.
It sounds like you either entered a zero for box 2a when it was blank or the 1099-R is incorrect.
You should check with the issuer of the 1099-R.
With regard to the Form 1099-R provided by the payer, if it has code 3 (Disability) in box 7 and the distribution was received before the normal retirement date for the plan, the taxable amount of the distribution is reportable on 2017 line 7 as wages, not on line 16 as a pension distribution. If the taxable amount is truly zero as is indicated by $0 in box 2a and box 2b Taxable amount not determined being marked, this presents a situation where the IRS will not see that the distribution has been properly reported because it will appear nowhere on your filed tax return. This situation would require a separate explanation statement describing why the distribution is not taxable. (The IRS often fails to recognize these as being reportable as wages rather than as pension even when the amount is reported as fully taxable.)
If the distribution was received after the normal retirement date for the plan, it goes on line 16. The gross amount of the distribution would be included on line 16a but the $0 taxable amount would mean that none of it would appear on line 16b. However, in most cases where a distribution was received after the normal retirement date of the plan I would expect the Form 1099-R to have code 7 instead of code 3.
The 1099R does show up on my tax return but not on line 16.
Then exactally where does it show up?
Are you over the youngest age that you could retire if you were still working? With a code 3, TurboTax will ask if you are older or younger than that age. As dmertz said, if younger then any taxable amount would go online 7 as wages and if box 2a was zero then there would be no entry at all. If older then the box 1 amount would be on line 16a.
Age 45 at the time the taxes were done
Then where do you see anything on your tax return at all?
If you are age 45 then that is under normal retirement age so a code 3 1099-R with a zero in box 2a will not appear anywhere on a tax return since there is nothing to report.
I still suggest that you talk to the trustee of the plan to confirm that is should not be taxable. Most disability pay that I know of is fully taxable as ordinary income. (particularly since box 2b is checked). The IRS probably believes that it is taxable which is why you received the letter. If your circumstance actually makes it not taxable then I recommend getting a letter from the plan trustee stating that so you can use the letter to answer (dispute) the IRS letter.
(Having zero in box 2a and box 2b checked is inconsistent. Box 2b means that the issuer could not determine the taxable amount, but zero in box 2a says that they *did* determine the amount. It cannot be both. The 1099-R instruction state that if box 2b is checked then box 2a must be BLANK - not zero unless it is an IRA which this is not.).