It has to break out and list the 10% early withdrawal penalty separately on your return.
You didn't actually pay the tax or 10% penalty (you pay a 10% early withdrawal penalty if you are under 59 ½). You had taxes withheld like from your paycheck. You still have to enter the whole amount (before taxes were withheld) with your other income to figure out the total tax (and it may put you into a higher tax bracket) and then the withholding is subtracted from the total tax to figure your refund or tax due. The withholding will show up on 1040 line 64 (2013 line 62) or 1040A line 36. The 10% penalty is on 1040 line 59 (2013 line 58).
The questions about exceptions to the penalty do not come after entering the 1099-R. Rather, you will see that area after you have finished all the Deductions and Credits section.
To enter the exception, starting from the "Federal Taxes" tab, select "Deductions & Credits". Select "Choose Explore on my own or I'll choose what to work on ." At the end of the Deductions & Credits section, select the "Done with Deductions" button. After several screens (depending on what entries you've made) you will come to the “Penalty May Apply” screen. Here you can pick the exception.
Do you need to know how to enter a 1099R?
You can just type 1099R into the search box at the top of your return, then find and it will give you a Jump To link to go right to it.
OR
Enter a 1099R under
Federal Taxes Tab
Wages & Income
Choose Jump to Full List -or I'll choose what I work on,
Then scroll way down to Retirement Plans and Social Security,
Then IRA, 401(k), Pension Plans (1099R) - click Start or Update
Pick the right kind of 1099R you have and on the same screen be sure to pick which person it is for if you are filing a Joint return.
After you enter the 1099R be sure to answer all the follow up questions on the next screens to determine how much is taxable or not. Go all the way to the end of the section. You have to enter it from the 1099R because there are codes on it you need to enter properly.
