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EndNote referencing software

How to use EndNote 21 and 20 Desktop for Windows and Mac, EndNote Online (Web) and EndNote for iPad and iPhone, thesis and publications writing, advanced tools, output (referencing) styles, syncing, sharing and collaboration, common issues and trouble

Convert to plain text option for documents saved on cloud storage

Always make a backup copy of your document.

For cloud saved documents, EndNote will not automatically save a second copy when converting to plain text.

If you choose continue on the message window, EndNote will remove all EndNote code from your original document

Convert to plain text message for cloud storage documents

To safely convert to plain text on cloud saved documents:

  1. Make a copy of your document and give it an appropriate name e.g. Thesis-Final-plain-text-version 16042024.docx. Do not convert your original document to plain text.
  2. Go to the copy.
  3. In the EndNote toolbar, click Convert citations and bibliography > Convert to plain text (Windows) or Tools > Convert to plain text (Mac).
  4. When the message appears, choose Continue (only if you are converting your copy to plain text).

EndNote toolbar disappeared in Word

The EndNote toolbar (or CWYW - Cite While You Write tool) may not install correctly or it may have disappeared from Word.


Install the EndNote (CWYW) tools

Reinstall EndNote (CWYW) tools that have disappeared


In-text references and reference list not updating correctly

This issue can be caused by different things. 

Track changes

Important Avoid using track changes if possible. It can interfere with EndNote references updating correctly.

  1. Accept all changes and delete all comments (when ready) in Track Changes.
  2. Click Update citations and Bibliography in EndNote tools.
  3. Check your in-text references and reference list for errors.

Word document may be corrupted

Check if it is your document or an issue with Word itself.

  1. Open a new Word document.
  2. Insert one or two references.
  3. Click Update bibliography and citations.
  4. If the references and reference list work correctly in the new document, your original document has become corrupt.

A corrupt document can be caused by:

  • using cut and paste, Delete or Backspace keys to delete references.
  • Track changes.

Important Best practice is to use the Remove Citations option in Edit and Manage Citations.

Fix a corrupted Word document

Repair damaged field codes in a Word document has steps to help fix this issue.

Journals names misplaced when exporting

Try this suggestion if you have trouble importing references from Google Scholar or any other database, and the journal name is being misplaced.

Library damaged or corrupt

Cloud storage can cause your library to become damaged. 

EndNote libraries should not be:

  • saved on the cloud e.g. DropBox, UQ RDM, iCloud, Google Drive, OneDrive
  • opened or worked on while stored on the cloud.

Important Regularly backup your library in case of issues.

Move your library

  1. Move your library to your local drive in a EndNote specific folder e.g. EndNote Library. Note: Don't use "EndNote" as the folder name as it used by the program to store output styles.
  2. Make sure it is not in an area automatically backed e.g. Mac OS to iCloud.
  3. Open any Word documents and your library.
  4. Click Update citations and bibliography in Word to sync to the library.

Repair a damaged library

Fixing a corrupt library has instructions on repairing a damaged library.

Further information

Mac M1 users

  • M1 Macs users may get an error message such as "Word wasn't able to load an add-in. Your add-in isn't compatible with this version of Word".
  • Office 365 version v16.46 has a compatibility issue with the current EndNote CWYW version.

Try these steps

  1. Quit EndNote and Word.
  2. Open Finder and go to the Applications folder.
  3. Highlight the Microsoft Word app file by clicking on it once. Note: You do not need to launch Word, just highlight it.
  4. Go to the File menu at the top of your screen and choose Get Info.
  5. Under General, check the option for Open using Rosetta.
  6. If these steps don't fix the issue you can contact AskUs to downgrade your MS office version to be compatible with EndNote. Note: EndNote will work for users with x86 Intel Macs updated to Office 365 v16.46.

Reference not found

This issue can happen when:

  • a reference doesn't format correctly e.g. it appears as {Ardila, 2014 #238}
  • the window below appears after updating or inserting a reference.

Screenshot of Selecting Matching Reference window from EndNote 20 for Windows by Clarivate.

Click on image for a larger version.

This can happen if:

  • a reference has been deleted from your library
  • a duplicate of that reference has been deleted
  • you are using different libraries to insert references.

Fix options

Deleted reference

  1. Check your Trash group. 
  2. Right click on reference if listed. 
  3. Select Restore to Library.
  4. In Word, click Update citations and bibliography.

Duplicate reference deleted

  1. EndNote 20 Select Matching Reference window may appear.
  2. Check for reference and select it, if listed.
  3. You can also search for the reference.
  4. Click on Insert.

Different libraries used to insert references

Important Only use one library with one Word document.

  1. Add the reference to your library. Update your document in Word.
  2. Select or search the reference from the EndNote [x] Select Matching Reference window.
  3. Select the reference and click Insert.
  4. Make sure you use the same library for that document.

Syncing to the wrong library

To sync to a different library, you need to reset or break the sync.

Reset the sync

Trial version installed

  1. If a trial version of the EndNote software becomes installed, and you are asked for the product code, uninstall.
  2. Download The University of Queensland licenced version (current UQ students and staff).
  3. Install.

Space appearing before in-text number for numbered styles

With numbered styles e.g. Vancouver, if you convert your document to plain text, a space can be added between the end of the sentence and the in-text number when converting your document to plain text.

Before converting to plain text, it appears as:

Video provides a powerful way to help you prove your point.1

After converting to plain text, it appears as:

Video provides a powerful way to help you prove your point. 1

Space between superscript citation and a word has instructions on how to fix this.

  1. Go to Word.
  2. Click on File.
  3. Select Options then click on Advanced.
  4. Move down to the Cut, copy and paste section.
  5. Click on the Settings button.
  6. Uncheck the option for Adjust sentence and word spacing automatically.
  7. Click OK.