What IRS Form 990-T (2016) Is For

Form 990-T (2016) is used by tax-exempt organizations to report unrelated business income tax (UBIT) and calculate tax liability on income from activities not substantially related to their exempt purpose. Organizations must file if they had $1,000 or more in gross unrelated business income during the 2016 tax year (IRS Instructions for Form 990-T (2016)).

When You’d Use Form 990-T for 2016 (Late or Amended Filing)

You would file Form 990-T for 2016 as a late or amended return if you received IRS notices about unfiled returns, discovered unreported unrelated business income, or needed to correct errors on a prior filing. The original due date was May 15, 2017 (or the 15th day of the 4th month for employee trusts like IRAs). Refund claims had to be filed by May 15, 2020, unless extended.

Key Rules Specific to 2016

• Hospital facility excise tax: New requirement on non-compliant facility income reported on Line 39.
  
  
• Section 179D deduction: Available for energy-efficient commercial property placed in service by December 31, 2016.
  
  
• American Samoa credit: Available only for tax years starting after December 31, 2015 and before January 1, 2017.
  
  
• NOL rules: Losses could be carried back two years and forward 20 years, with no siloing requirement.
  
  

Step-by-Step (High Level)

• Gather IRS account transcripts and financial records for 2016.
• Use the 2016 version of Form 990-T—never substitute with current forms.
• Attach all required schedules (A–K) and detailed statements for NOLs.
• Mark “Filed Late” or “Amended Return” at the top, with explanations.
• Mail to IRS Service Center, Ogden, UT 84201-0027.
• Keep complete records and proof of mailing.

Common Mistakes and How to Avoid Them

• Wrong form year: Use only 2016 forms; line numbers and requirements differ from later years.
  
  
• Overlooking NOL carrybacks: 2016 losses could offset 2014–2015 income if timely claimed.
  
  
• Penalty miscalculations: 5% per month (up to 25%) for late filing; $205 minimum after 60 days.
  
  
• Inadequate documentation: Always include detailed NOL and debt-financed income schedules.
  
  
• Wrong filing address: Use the Ogden, UT address specified in 2016 instructions.
  
  
• Ignoring estimated tax rules: Penalties apply if tax liability exceeded $500 and quarterly payments were insufficient.
  
  

What Happens After You File

The IRS typically processes returns within 6–8 weeks, though late or amended 2016 filings may take longer. Expect notices for balances due, penalties, or requests for clarification. If you owe tax but cannot pay, you may request an installment agreement using Form 9465. Interest and penalties accrue from the original due date. If you disagree with IRS determinations, you can appeal informally or through the IRS Appeals Office.

FAQs

Can I still get a refund for my 2016 Form 990-T?

Generally no, as the standard three-year refund statute expired on May 15, 2020. However, exceptions may apply if you filed amended returns addressing major errors or if tax was paid within the past two years. In most cases, refunds are unavailable, but late filing still helps reduce exposure to penalties and compliance risks.

What penalties will I face for filing 2016 late in 2025?

You may face 5% of unpaid tax per month, capped at 25%, plus late payment penalties of 0.5% per month. Interest accrues daily from the original due date until the balance is paid. The IRS may grant penalty relief for reasonable cause, such as reliance on a tax professional, natural disasters, or illness.

Do I need to get tax transcripts before filing?

Yes, transcripts provide valuable insight into your account. They show prior filings, IRS notices issued, assessed penalties, and payment history. Reviewing transcripts before filing helps avoid duplicate reporting and ensures you understand your current IRS status. This is especially useful if you are filing multiple years of overdue returns at once.

Should I also amend my state exempt organization returns?

Often yes. Many states conform to the federal definition of unrelated business income and require amended returns if your federal filing changes. State requirements and deadlines vary, so check with your state tax agency. Failing to amend state returns can lead to penalties, additional assessments, or suspension of state charitable registrations.

Can I e-file a 2016 Form 990-T now?

No, e-filing is only available for current and recent tax years. For 2016, you must file a paper return and mail it to the Ogden, UT processing center listed in the original instructions. Ensure you use certified mail or an approved private delivery service so you have proof of timely submission.

How do 2016 NOL rules differ from today?

In 2016, NOLs could be carried back two years and carried forward up to 20 years. Losses from one business could offset unrelated business income from another, since the TCJA “siloing” rules were not yet in effect. Today, most carrybacks are eliminated, carryforwards are indefinite, and losses must be tracked by activity.

What if I discover I should have filed 2016 but never did?

File as soon as possible. The IRS can assess penalties and tax indefinitely if no return was filed. Submitting now starts the statute of limitations clock and may qualify you for penalty abatement. Filing demonstrates good faith compliance and helps protect your organization’s tax-exempt status from automatic revocation.