Table of Contents

1099 E-Filing: Missouri

Nina Tchistiakova Updated by Nina Tchistiakova

Due date

March 1

E-filing threshold

No Requirement

Filing options

Electronic filing

Forms to file

State requires 1099-B, 1099-DIV, 1099-INT, 1099-MISC, 1099-NEC, 1099-PATR and 1099-R

Transmittal form

Form MO-W3 Located in CFS Payroll System under “W-2/1099 Information Returns”

Required file name


E-filing website

Submitting files

Before you process a file you must complete Form MO-W3 located in CFS Payroll System under ''W-2/1099 Information Returns'' and save the form to process 1099's for Missouri. The RV record in the file contains all of the data from the MO-W3. When you process the file you will be given the option to select a saved MO-W3. Do not include the paper MO-W3 with your submission. 

· If you are a Missouri employer with an active employer withholding account, use the current Missouri Tax ID and PIN number to gain access.

· If you do not know your Missouri Tax ID or PIN number, you can contact our taxpayer assistance phone lines by telephone at 573-751-7200, by email email to, or by fax at 573-522-1722.

· You will receive a confirmation number after the file is successfully uploaded. Keep this confirmation number for your records.

Third party payroll agencies filing for Missouri clients, that do not have a Missouri Employer Withholding account and did not register with us last year, will need to send an email to to request an MO-W3 Submission Account. Please include the responsible person’s name, email address, and phone number in your request.

NOTE: If you have already registered for the EFW2 submission you do not need to register again for the 1099's.

When a file cannot be processed, the user will be notified by email, any reject is a reject of the entire file. The email will contain a subject of “EF1099 Rejected”, the email will include recommendations on how to correct the file. When resubmitting a file after a reject be sure to upload the entire file, as if you are submitting for the first time.

Prior years 2017 and earlier data must be submitted by paper.

If state taxes were withheld, the compact disc, flash drive, or paper 1099s must be accompanied by the Transmittal of Wage and Tax Statements (Form MO W-3). If state taxes were not withheld, a copy of Federal Form 4804 must accompany the compact disc or flash drive or Federal Form 1096 must accompany the paper 1099s.

We cannot process corrections electronically. If after you have filed your Form 1099(s) and Form MO W-3, you discover an error in amount of Missouri Withholding on the original 1099(s), you must correct it by remitting an amended Form MO-941. This form must be used to increase or decrease any previously reported tax amounts. Attach a copy of the corrected Form 1099(s) to the amended Form MO-941 and Form MO W-3. If you have discovered an incorrect figure was indicated on the Missouri Department of Revenue 14 original Form MO W-3; however, no changes need to be made to the amount of withholding: submit a new Form MO W-3 with the correct figures and check W-3 Corrected on the top left corner. Note: Do not send copies of 1099(s), if no change in withholding tax liability.

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