Was a 2003 claim for refund on an amended 1999 New York personal income tax return, filed after the original return itself was filed late, timely under the Tax Law's statute of limitations?

Plain-English summary

Michael P. Marotta filed and paid the balance due on his 1999 New York State personal income tax return late - on August 21, 2001 - because he was a shareholder in a Virginia S corporation that had not given him his tax information in time, and Virginia had made an error on his return that led him to pay Virginia additional tax. Believing that fixing the Virginia error meant he had overpaid his 1999 New York income tax, Marotta filed an amended 1999 New York return in 2003 claiming a refund. He asked the Department whether that 2003 refund claim was filed on time.

The Department walked through the refund statute of limitations in Tax Law § 687(a): a claim for credit or refund of an overpaid income tax must be filed within three years from when the return was filed, or two years from when the tax was paid, whichever period ends later. Because Marotta's 1999 return was both filed and paid on the same day - August 21, 2001 - his three-year window ran until August 21, 2004. Since he filed his refund claim in 2003, well before that deadline, the claim was timely.

The Department also flagged the separate look-back rule in § 687(a): even a timely claim only supports a refund of tax paid within the three years immediately preceding the claim (plus any filing extension). Because Marotta's tax was paid on the same date his return was filed, that payment fell comfortably within the three-year look-back period, so the timing rules did not by themselves limit the amount he could potentially recover.

Importantly, the opinion decided only the timeliness question. It expressly did not decide whether Marotta actually overpaid his 1999 New York tax, and it did not address whether he owed - or could still be assessed - penalties and interest for filing his 1999 return and paying his 1999 tax late.

What this means for you

If your original return was filed late

A late-filed original return does not by itself disqualify a later refund claim. Under Tax Law § 687(a), the three-year clock for filing a refund claim runs from the date you actually filed the return (or two years from when you paid the tax, if that is later) - not from the return's original due date. Filing late can shrink your effective window compared to a taxpayer who filed on time, but it does not eliminate it.

If you're correcting a New York return because of an out-of-state tax adjustment

Discovering an error on another state's return - and paying that state additional tax - does not automatically create a New York refund right. This opinion addressed only whether the claim was timely; it did not confirm that fixing a Virginia error actually produced a New York overpayment, and it left penalty-and-interest exposure for the late 1999 filing and payment completely open.

Common questions

Q: Marotta's original 1999 return was filed late - did that make his 2003 refund claim untimely?
A: No. Tax Law § 687(a) measures the claim deadline from the date the return was actually filed (or from when the tax was paid, if later), not from the original due date. Since he filed and paid on August 21, 2001, he had until August 21, 2004 to file a claim, and his 2003 claim was well within that period.

Q: Does filing a timely claim guarantee the full refund amount will be paid?
A: Not automatically. Tax Law § 687(a) caps any refund at the tax paid within the three years immediately preceding the claim (plus extensions). Here, because the tax was paid the same day the return was filed, that payment was within the three-year look-back, so timing alone did not cap the potential refund.

Q: Did the Department confirm that Marotta actually overpaid his 1999 New York tax?
A: No. The opinion addressed only the timeliness of the claim; it explicitly stated it did not decide whether an overpayment actually occurred.

Q: Were penalties and interest for the late 1999 filing and payment addressed?
A: No. The opinion expressly noted it did not address whether penalties and interest were owed for the late filing of the 1999 return or the late payment of the 1999 tax liability.

Citations and references

• Tax Law § 651(a) - sets the due date (fifteenth day of the fourth month after the taxable year closes) for filing a personal income tax return
• Tax Law § 686(a) - allows the Commissioner to credit an overpayment of income tax (with interest) against other liabilities before refunding any balance
• Tax Law § 687(a) - requires a refund/credit claim within three years of filing the return or two years of paying the tax, whichever is later, and caps the refundable amount to tax paid within the three years (or two years) preceding the claim
• Tax Law § 687(e) - bars any credit or refund once the applicable limitations period expires without a timely claim
• Tax Law § 687(i) - deems certain prepaid income tax (withholding, estimated payments) paid on the original return due date

Source

• Landing page: https://www.tax.ny.gov/pubs_and_bulls/advisory_opinions/income_ao_2004.htm
• Opinion: https://www.tax.ny.gov/pdf/advisory_opinions/income/a04_8i.pdf

Original ruling text

New York State Department of Taxation and Finance

Office of Tax Policy Analysis
Technical Services Division

TSB-A-04(8)I
Income Tax
November 22, 2004

STATE OF NEW YORK
COMMISSIONER OF TAXATION AND FINANCE
ADVISORY OPINION

PETITION NO. I040830B

On August 30, 2004, a Petition for Advisory Opinion was received from Michael P.
Marotta, 528 W46th Street, Apt 2E, New York, New York 10036.
The issue raised by Petitioner, Michael P. Marotta, is whether Petitioner timely filed a
claim for refund on an amended 1999 New York State personal income tax return.
Petitioner submits the following facts as the basis for this Advisory Opinion.
Petitioner filed and paid the balance due on his 1999 New York State personal income
tax return on August 21, 2001. This late filing was due to the fact that Petitioner is a shareholder
in a Virginia S corporation, which did not furnish him tax information before this time. There
was an error on Petitioner’s Virginia return. Petitioner owed additional tax, and has
subsequently filed and paid the appropriate taxes, to the commonwealth of Virginia.
Consequently, Petitioner believes that he has overpaid his New York income tax liability
for 1999. In 2003, Petitioner filed an amended New York tax return for tax year 1999 to reflect
this overpayment.
Applicable law
Section 651 of the Tax Law provides, in part:
(a) General. On or before the fifteenth day of the fourth month following the close of the
taxable year, an income tax return under this article shall be made and filed by or for:
(1) every resident individual (A) required to file a federal income tax return for the
taxable year,...
Section 686(a) of the Tax Law provides:
General. – The commissioner of taxation and finance, within the applicable period of
limitations, may credit an overpayment of income tax and interest on such overpayment against
any liability in respect of any tax imposed by this chapter on the person who made the
overpayment, against any liability in respect of any tax imposed pursuant to the authority of this
chapter or any other law on such person if such tax is administered by the commissioner of
taxation and finance and ... against past-due support, a past-due legally enforceable debt, and

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Income Tax
November 22, 2004
against the amount of a default in repayment of a guaranteed student, state university or city
university loan. The balance shall be refunded by the comptroller out of the proceeds of the tax
retained by him for such general purpose. Any refund under this section shall be made only
upon the filing of a return and upon a certificate of the commissioner of taxation and finance
approved by the comptroller. The comptroller, as a condition precedent to the approval of such
a certificate, may examine into the facts as disclosed by the return of the person who made the
overpayment and other information and data available in the files of the commissioner of
taxation and finance.
Section 687 of the Tax Law provides, in part:
(a) General. – Claim for credit or refund of an overpayment of income tax shall be filed
by the taxpayer within three years from the time the return was filed or two years from the time
the tax was paid, whichever of such periods expires the later, or if no return was filed, within two
years from the time the tax was paid. If the claim is filed within the three year period, the
amount of the credit or refund shall not exceed the portion of the tax paid within the three years
immediately preceding the filing of the claim plus the period of any extension of time for filing
the return unless such claim is for a credit or a portion thereof provided pursuant to paragraph
two or four of subsection (c), paragraph two or four of subsection (d) or subsection (e) of section
six hundred six of this chapter. If the claim is not filed within the three year period, but is filed
within the two year period, the amount of the credit or refund shall not exceed the portion of the
tax paid during the two years immediately preceding the filing of the claim unless such claim is
for a credit or a portion thereof provided pursuant to paragraph two or four of subsection (c),
paragraph two or four of subsection (d) or subsection (e) of section six hundred six of this
chapter....
*

*

*

(e) Failure to file claim within prescribed period. – No credit or refund shall be allowed
or made, except as provided in subsection (f) of this section or subsection (d) of section six
hundred ninety, after the expiration of the applicable period of limitation specified in this article,
unless a claim for credit or refund is filed by the taxpayer within such period....
*

*

*

(i) Prepaid income tax. – For purposes of this section, any tax paid by the taxpayer before
the last day prescribed for its payment, any income tax withheld from the taxpayer during any
calendar year, and any amount paid by the taxpayer as estimated income tax for a taxable year
shall be deemed to have been paid by [the taxpayer] on the fifteenth day of the fourth month
following the close of [the taxpayer’s] taxable year with respect to which such amount
constitutes a credit or payment.

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TSB-A-04(8)I
Income Tax
November 22, 2004

Opinion
Pursuant to section 651(a)(1) of the Tax Law, the due date of Petitioner’s 1999 New York
personal income tax return was April 17, 2000, (or April 18, 2000, if Petitioner’s federal income
tax return was required to be filed at the IRS Service Center in Andover, Massachusetts) since
April 15, 2000, was a Saturday. However, Petitioner did not file his return and pay the tax due
until August 21, 2001. Subsequent to the filing of Petitioner’s 1999 New York income tax
return, Petitioner discovered that an error was made in computing income tax due to the
Commonwealth of Virginia for tax year 1999 and Petitioner paid additional tax to Virginia for
tax year 1999.
Petitioner believes that as a result of this increase in the Virginia tax liability for 1999,
Petitioner’s 1999 New York income tax liability was overpaid. Pursuant to section 686(a) of the
Tax Law, within the applicable period of limitations, an overpayment of income tax and interest
on such overpayment may be credited by the Commissioner of Taxation and Finance against any
of the following liabilities, if any, of Petitioner: a liability in respect of any tax imposed by the
Tax Law, a liability in respect of any tax imposed pursuant to the authority of the Tax Law or
any other law if such tax is administered by the Commissioner of Taxation and Finance, and a
liability for past-due support, a past-due legally enforceable debt and the amount of a default in
repayment of a guaranteed student, State university or city university loan. The balance of any
overpayment shall then be refunded to Petitioner.
Pursuant to section 687(a) of the Tax Law, a taxpayer may file a claim for credit or
refund of an overpayment of income tax for tax year 1999 within three years from the time the
return was filed. Since the return was filed August 21, 2001, Petitioner may file a claim for
credit or refund on or before August 21, 2004. However, the amount of credit or refund allowed
may not exceed the portion of the tax paid within the three years immediately preceding the
filing of the claim plus the period of any extension of time for filing the return. In this case,
Petitioner filed his 1999 return on August 21, 2001, and, in 2003, he filed a claim for credit or
refund of an overpayment of income tax for tax year 1999.
Accordingly, Petitioner filed his claim within three years from the time his return was
filed. However, if it is determined that Petitioner has overpaid his income tax for tax year 1999,
section 687(a) of the Tax Law limits the amount of any credit or refund of such overpayment to
the portion of the tax Petitioner paid within the three years immediately preceding the date
Petitioner filed the claim plus the period of any extension of time, if any, for filing the return.
Note that this Advisory Opinion does not address the question of whether Petitioner has
actually overpaid his New York income tax liability for tax year 1999, and it does not address the

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Income Tax
November 22, 2004
issue of whether penalties and interest are owed for late filing Petitioner’s 1999 tax return and for
late payment of Petitioner’s tax liability for tax year 1999.

DATED: November 22, 2004

NOTE:

/s/
Jonathan Pessen
Tax Regulations Specialist IV
Technical Services Division

The opinions expressed in Advisory Opinions are
limited to the facts set forth therein.