My employer has been deducting New York City taxes from my paycheck since 2004 and I have not been a NYC resident since 2003. I have recently cleared up the issue with my employer, however they would only refund me for this years NYC tax deductions. I assume that I need to file a New York State ammendment. Do I also have to file a federal ammendment as well? Is there an easier way to go about this? :confused: Thank you in advance.

You need only file amendments to your NY state return to get the NYC taxes refunded.

However, it is TOO LATE for 2004 and 2005. Most states (NY state among them) honor the same three-year statute of limitation that the IRS imposes for claiming refunds, which means you have until 15 April 2010 to claim the refunds for the 2006 tax return.

Please clarify something - when you filed your NY State income tax returns did you report that both NY State and NY City tax had been withheld? Both the NY State and NY City withheld amounts are shown on your W-2 form each year, so hopefully you reported both numbers on your return. See the attached instructions - I'm asking about the entry you made (or should have made) on line 47 (see page 28 of the instructions). Now, since both the NYS and NYC taxes are calculated on a single tax return, if you properly reported the amounts of both state and city taxes that were withheld, then you're OK - the amounts withheld for both NYC and NYS withholding would have gone to pay just the NY State tax you actually owed. If this is what you did then all is well and there is no need to file amended returns.

However, if you did not report any NY City tax withheld on line 47, then you should file amended returns as ATE suggests. You'll have to include copies of your old W-2's to document that there was NYC withholding that you did not include on your original returns.

http://www.tax.state.ny.us/pdf/2008/inc/it150_201i_2008.pdf