NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.

NIH Manuscript Submission Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005-.

Cover of NIH Manuscript Submission Help

NIH Manuscript Submission Help [Internet].

Show details

The NIHMS System User’s Guide to Submitting a Manuscript

Created: ; Last Update: September 8, 2010.

On May 2, 2005, The National Institutes of Health (NIH) Public Access Policy went into effect for NIH-funded researchers to submit their peer-reviewed manuscripts—only those that have been accepted for publication—to PubMed Central (PMC).

To facilitate this submission process, the NIH developed the NIH Manuscript Submission System (NIHMS) as a way to manage your manuscript submissions.

Your manuscript can be submitted in a wide range of electronic formats. Additional files, such as figures, tables, or supplementary information, should also be included with your manuscript submission. You do not need to format your manuscript beyond the requirements of the journal that has accepted your article.

This user’s guide gives you step-by-step instructions on how to submit and approve manuscripts so that they may be placed in PMC for permanent archiving.

If you find that you have additional questions or would like to submit comments regarding the NIHMS System, please contact the NIHMS Help Desk (vog.hin.mln.ibcn@pleh-smhin).

Log In to the NIHMS System

From, there are several ways for a submitter to log in to the NIHMS System.

To begin, look for the yellow box at the right side of the screen and click on “Proceed” to log in.

The best log in route to use depends upon the submitter’s occupation and existing account information:

  • eRA Commons – for NIH extramural principal investigators, grantees, or applicants with an eRA Commons account
  • NIH – for NIH intramural scientists and NIH staff
  • Publisher – for publishers
  • HHMI – for Howard Hughes Medical Institute investigators
  • myNCBI – for others and those who need to create a new account

Note: Use the same login option for all visits to the NIHMS System to avoid creating duplicate accounts. If a single user creates separate logins, not all of the user’s submissions will be consolidated but will be distributed among the different login accounts, thus creating confusion.

Image users-Image001.jpg

To Log In as a Reviewing Author or Author’s Proxy:

eRA Commons – for NIH extramural PIs, grantees, or applicants

The NIH eRA Commons is a Web-based system for NIH extramural grantee organizations, grantees, and the public to receive and transmit information electronically. To be able to use the NIH eRA Commons route, you must be registered as a user. Contact your Office of Sponsored Programs or Office of Clinical Research representative for information about registering for an eRA Commons account.

NIH – for NIH intramural scientists and NIH staff

The NIH Login may be accessed and used only for authorized government business by intramural personnel. If you are employed by NIH, this is the place to log in to the NIHMS System.

HHMI – for Howard Hughes Medical Institute investigators

Researchers who received funds from the Howard Hughes Medical Institute use this route to log in to the NIHMS system.

My NCBI – for others

Anyone can register for an account through My NCBI, including members of the public. This system is not recommended for NIH extramural PIs, grantees, and applicants (who should use eRA Commons) or for NIH intramural scientists (who should use the NIH login). My NCBI is especially useful for those submitting a manuscript on behalf of the PI. For instance, if the PI wants a colleague or assistant to submit a manuscript but does not want the submitter using a personal account login and password, the manuscript should be submitted via a My NCBI account.

To Log In as a Publisher:

A publisher submitting articles to the NIHMS System should log in using the system designed specifically for publishers to use. The publisher log in process is quick, and easy for multiple submissions. To obtain a publisher login account, please contact the NIHMS Help Desk (vog.hin.mln.ibcn@pleh-smhin).

Overview of the Submission Process

There are four steps involved in submitting your manuscript to the NIHMS System:

  • Set up the manuscript – provide bibliographic information and NIH Intramural grant or project information
  • Submit manuscript files – upload all manuscript files, including figures, tables, and supplementary information
  • Approve the PDF Receipt – review a PDF version of your manuscript to ensure that we have received all of the content and approve the NIHMS submission statement
  • Approve the Web Version – review and approve the new Web version of your manuscript for use in PubMed Central (PMC)

Submitting a New Manuscript

Step 1: Journal & Title

Here you must enter the name of the journal in which the accepted manuscript will be published. There are three ways to enter your manuscript’s journal and title information:

  • Enter Manually: Manually entering the journal name and manuscript title is the default method to complete Step 1 of your submission to NIHMS. As you begin to type the journal name, a suggestion box will appear with the names that are similar to what you are typing. Choose the journal name from this list. If the journal name does not appear in this list, you may enter the complete name as free text.
  • Lookup Article: If the citation for your manuscript is available in PubMed, you may use the “Lookup Article” function to search for it. First, click on the “Lookup Article” tab. (Please note that PubMed indexes abstracts only. PMC archives full-text research articles and is linked to PubMed. Manuscripts submitted to the NIHMS system will be prepared for archiving on PMC as well as indexed in PubMed.) From this tab, you may enter a free-text PubMed query (including Boolean terms and PubMed filters, if desired) in the text box next to the “Search” button. Your last 5 search terms are offered as hyperlinks to initiate searches as well as “Quick search” terms based upon your name and any grants associated with your login. When you find your PubMed citation, select the radio button next to it and click on the “Next: Grant Info” button on the lower right of the page to continue.
  • My NCBI Bibliography: If you have a saved Bibliography associated with a My NCBI account, you may use this list to select from. First, click on the “My NCBI Bibliography” tab. You may be asked to sign in to your My NCBI account. Once you are signed in to your account, your saved Bibliography will be displayed. Manuscripts that have already been submitted or are already archived in PubMed Central will be noted in the “Status” column. Select the radio button next to a citation that is eligible for submission to the NIHMS and click on the “Next: Grant Info” button on the lower right of the page to continue.

At this point, you can “Save & Exit,” “Cancel Submission,” or move on to Step 2 by clicking on the “Next: Grant Info” button.

Step 2: Grants/Projects

Here you enter the grant information required for the submission. Each manuscript submitted must be assigned at least one grant, project number, or other source of NIH funding. NIHMS cannot process a manuscript that did not derive from NIH funding. You can enter the grant or project number or the first and last name of the PI.

When you click the “Search” button, if the NIHMS System finds a match, it will appear on the screen. Sometimes the NIHMS System will find several matches, depending on how the information is entered, and you can choose the correct grant from a list.

Image users-Image002.jpg

When you are finished entering all of the NIH grant information and want to continue with the submission, click on the “Next: Upload Files” button.

Step 3: Files

Here you will find information on what files to include (please include all supplemental materials and videos, if any are associated with the manuscript), the list of acceptable formats, and how to label each file uploaded. There are three things you must enter to upload a file:


Type of file (i.e., text, figure, supplement, etc.)


Label of file (i.e., supplemental video 3, figure 1)


Name of file – automatically filled in when the user clicks “Browse” to access his or her computer and designate a file for uploading

You can keep adding files as needed by clicking the purple “Add another” file link. When you are finished collecting the files, click the “Upload Files” button. A window will pop up to show the progress of the upload.

Image users-Image003.jpg

When all files have been successfully uploaded, the screen will refresh. When you have finished uploading files, click the “Next: Summary” button.

Step 4: Summary

Here you have a chance to review all the information just entered for this submission.

Image users-Image004.jpg

If you need to make any changes, navigate back to the previous pages to edit your information. If the information entered is accurate and complete, click the “Next: PDF Approval” button.

Step 5: PDF Approval

This is the final part of the submission process. However, if the person submitting the manuscript at this time is not the Reviewing Author but instead a Submitter (or Author Proxy), he or she will not be able to move to the final step. Only the Reviewing Author can approve the submitted manuscript and complete the submission. At this stage, the Submitter (or Author Proxy) will be able to assign the author as the reviewer of the manuscript.


Review: Click on the highlighted PDF Receipt file and view it before approving it. Be sure all of the pieces of the manuscript are there, including supplemental files and/or videos (a mention of these types of files will appear on a mostly blank page at the end of the PDF receipt).


Certify Inclusion of Supplemental Files: Check this box to certify that all supplemental files associated with your manuscript have been included with your submission.


Choose a Reviewer: If you are not an author on the manuscript being submitted, you can designate the author that should approve the final materials going into PMC. That person will be informed, using the email address you provide, that they have been designated as the reviewer of this manuscript and will need to log into NIHMS to complete this submission. If you are an author on the paper and wish to review it, you will designate yourself as the reviewer. Note that this is the default option.


Set Release Delay: Set the release delay of the manuscript to PMC (up to 12 months). If you are not sure about your publisher’s policy about release (embargo) dates, contact the publisher before setting this delay.


Approve: Click on the green “Approve” button.


Submission Statement: On the next page, you will be asked to review the NIHMS submission statement. Read the statement and click either “Agree” or “Disagree” (clicking “Disagree” will place the submission on hold).

Image users-Image005.jpg

This stage of the submission is now complete and in the hands of the NIHMS System staff. Next, the process of preparing the manuscript for PMC takes approximately 2 weeks, depending on the complexity of the manuscript. When the Web version (PMC version) of the manuscript is available for review, the Reviewing Author will be notified via email. In the next stage of the NIHMS process, the Reviewing Author will need to approve or request corrections of the PMC-ready Web version of the manuscript created by NIHMS.

The Author Approves the Web Version

After the submitted manuscript has been processed and prepared for PubMed Central (PMC), an email will be sent to the Reviewing Author. The email will include a link that will take the author directly into the NIHMS System so that he or she can view and approve the Web version (both HTML and PDF) of the manuscript.

It is important for the Reviewing Author to view both the HTML and PDF formats and either approve both for posting on PMC (see Approve Web Version) or request corrections (see Request Corrections).

Image users-Image006.jpg

Approve Web Version


The Reviewing Author must click on the URL in the notification email received, or if that is not available, log in to the NIHMS System.


Once in the system, you will see the Manuscript List screen. The manuscript(s) you need to view and approve are listed at the top, below the section Manuscripts That Require Your Attention.


A Manuscript Status alert will appear next to the manuscript title that says “Waiting for author approval of final Web version of manuscript.”


Click on the hyperlinked manuscript title to access the Web version. This screen is called the “Review and Approve” screen.


In the next screen, you will see the link “PMC-ready Manuscript” highlighted in yellow with an arrow pointing to it. Click on this highlighted link to access the Web version of your manuscript. (The other hyperlinked file to the right of the highlighted Web version link, “Original Submission,” is the original submission PDF, which is for your reference only. The third hyperlinked file displays the web version of the PMC-ready “Manuscript with paragraph numbering.” You should use these paragraph numbers to indicate where any corrections need to be made. However, these paragraph numbers will not appear in the approved manuscript available on PMC.)


A new screen will appear showing the Web version of the manuscript. You will see the HTML first with the NIH Public Access logo at the top. Check carefully for errors and/or missing data.


In the upper part of the left frame, click on “PDF” to access the PDF version.


When you are finished viewing the Web version, close the screen. You will not be logging out of the NIHMS System by closing this screen because it is a separate screen from the NIHMS System.


You will return to the “Review and Approve” screen.


Click the green “Approve” button or click the blue “Request Corrections” button (see the next section).

Note: Visual guides are available on the NIHMS System website that provide instructions on how to view and approve the Web version. See Approve WEB Version.

Image users-Image007.jpg

Request Corrections

If you notice a formatting error or critical textual error in the Web version of the manuscript, please submit a request for corrections. Please note that only errors or omissions that impact the scientific accuracy of your article are eligible for correction. Please report all corrections at one time.

  • Follow the same instructions listed above in the Approve Web Version section to view the Web version of your manuscript. Then, after returning to the Review and Approve screen, click on the blue button “Request Corrections.” (Also see the visual guide Request Corrections on the NIHMS System website.)
  • In the text boxes, describe the required changes and where they are located:

    Click on the yellow hyperlink “Manuscript with paragraph numbering” to view your manuscript. This version will have all sections and paragraphs numbered.


    Use the highlighted paragraph numbering (if applicable) to describe the location of the error (e.g., P3, P27, S7, Title, Figure 2, References, Footnotes).


    Describe all required changes in detail in the correction box. Use a new box for each correction.


    Click the purple link “Add another Request for Corrections” if you need to add more text boxes to report corrections.

Note: Only errors or omissions that impact the scientific accuracy of your article are eligible for correction.

When you are ready to send the list of corrections, click the green “Send” button. The NIHMS System staff will be notified and sent your list of corrections. If the corrections are minor, the manuscript may be available for your review again in a few days. However, if the corrections are extensive or complex, the manuscript may need to be reprocessed, which can take from 1 to 2 weeks, depending on the corrections. The Reviewing Author will be notified when the Web version is once again available for his or her review.

Image users-Image008.jpg

Frequently Asked Questions (FAQs)

FAQs are available for:

NIH-funded researchers


Bookshelf ID: NBK3846
PubReader format: click here to try


Other titles in this collection

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...