The IRS Service Center will manually process your amended return. They will check to make sure your explanations are sufficient. They will check to see that you have sufficiently documented the changes in your tax return. For example, they will double check your W-2 statements, withholding, and other information reporting on your amended tax return. If the IRS needs more explanation or documentation, they will write you a letter and ask for the specific information they need. If you owe additional tax, you should mail in a check to pay the tax in full. If you are due an additional refund, expect your refund to arrive in approximately 8 to 12 weeks.
The fact that this is done manually, and that transmission to them has to be done by paper, is the reason it takes so long.
Here's a great article on the whole process by enrolled agent XXXXX XXXXX: http://taxes.about.com/od/taxtrouble/a/form1040X_3.htm
Also, here's what the IRS says, AND a way to check online regarding your return: http://www.irs.gov/Filing/Individuals/Amended-Returns-(Form-1040-X)/Wheres-My-Amended-Return-1
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