What is the penalty for filing Form 990 late?
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If the organization files its Form 990 after the due date (including any extensions), and the organization doesn't provide reasonable cause for filing late, the Internal Revenue Service will impose a penalty.
 
A penalty of $20 a day ($105 a day for large organizations) will be imposed for the late filing of Form 990. The same penalty is also applicable for failing to furnish the correct information unless the organization provides an attachment with an explanation to state that the late filing was due to a reasonable cause.
 
The penalty amount can go up to a maximum of $10,500 or 5 percent of the organization's annual gross receipts. For example, if the organization has gross receipts exceeding $1,084,000 for the year, the penalty is $105 a day, which can go up to a maximum of $54,000.