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EndNote: Troubleshoot & FAQ

If you're a Mac user, the first thing to try is opening Endnote, going to the 'Endnote X9' menu, and running Customizer.... This process will reinstall CWYW tools, and that should fix the problem.
If this doesn't fix the issue visit this helpful guide for Mac or this guide for PC from Clarivate.

Easy peasy: you just need to update your computer's file associations (to tell it to open RIS files with Endnote).

If you're a Mac user, follow the instructions at this link.

If you are using a PC, visit this helpful guide.
Windows users can also try the following steps:

  1. Right-click an RIS file and select ‘Properties’.
  2. In the pop up window it should have a field called ‘Opens with’ and there should be a ‘change’ button
  3. In this window, scroll down to Endnote and select it and hit OK.

This should update the settings across your system.

If you've set up Sync, the easiest thing to do is to create a New Library on your new device, and then sign in and run a Sync. This will download your Endnote Library from the cloud onto the new device.

If you haven't set up Sync, you can get more information on copying libraries between computers with this helpful guide from Clarivate.

This is happening because Word is trying to connect to Endnote online. It's really easy to fix.

  1. Go to the Endnote menu in Word and select 'Preferences'
  2. In the box that pops up, select the Application tab
  3. Currently, Word will have 'Endnote Online' selected. Change the selection to 'Endnote' and hit OK.

This happens because Endnote is looking at the wrong Styles folder. Endnote has a Styles folder that sits with the application, and another that it installs in your computer's 'Documents' folder.

To correct this, go to Preferences then select Folder Locations then click the 'Select' button under the 'Styles' section. Change the directory to 'Styles' in your Documents folder. This should fix the problem.

This issue is usually caused by having previously installed a piece of referencing software such as Mendeley. There are two types of COM exception error, with guides to fixing each linked below:

COM Exception: Cannot Edit Range
Other COM exception errors (on Mac)

There are a number of common causes for this issue: usually it relates to incorrect data in the reference in an Endnote library.

Corporate authors
If you are citing a company or government agency, you will need to put a comma at the end of the full organisation name in the Endnote Library reference. (eg. University of Sydney,)

Initials appearing in-text
This usually means that the same author is appearing in your Endnote Library with multiple naming conventions. To fix this, simply go through your library and make sure the author field is the same for all publications: eg. Stephen Ball and Stephen J. Ball are the same person - use one or the other in all references.

Changes to references aren't showing in the document
Go to the Endnote menu in Word and select update citations and bibliography.

References look strange and appear in curly brackets
This means your document is in unformatted citations mode. Go to the Endnote menu in Word and select update citations and bibliography

This is happening because Endnote is seeing {squiggly brackets} and assuming this is a citation that it needs to update.

Squiggly brackets are the way Endnote identifies ‘unformatted citations’, so removing these should stop the ‘select matching reference’ window from popping up.

To do this, try clicking cancel on the window, or if it continues to appear just hit ‘ignore all’. Then find the part of your paper that has {squiggly brackets} and change those squiggly brackets to [square] or regular parentheses. This should fix that problem and you can continue referencing as usual (to test it, after you’ve removed the squiggles just go to the endnote menu in word and select ‘update citations and bibliography’).

Unfortunately, the connection files that Endnote uses to connect to online searching haven't worked for some time now. We have raised this with Endnote, but this feature is pretty dated. The good news is you will have a better search experience using the Library's databases or Library Search using your usual web browser!

Ouch, this usually happens if a Library is stored in a cloud service like Dropbox or Google Drive. Make sure your Endnote Library is stored on your local hard drive. You can set up an Online Sync solution by visiting our Backup & Sync page in this guide.

To repair your Library, follow these steps:

  1. Open the Endnote application, and select Tools > Recover Library...
  2. In the dialogue that pops up, navigate to your broken Endnote Library and select it. Make sure you save the recovered Library on your local drive.

If that process doesn't work, check out this helpful guide to recovering your library files from Clarivate.

Sometimes you'll find that sync isn't working - Endnote might appear to Sync, but it doesn't update your online library (which you can check at If your sync seems to be broken, this is the procedure you should follow.

  1. Make sure you have a backup of your Endnote Library. You can either create a compressed library, or copy and paste your .enl library and associated .Data folder into a safe location.
  2. Open EndNote >click on Edit>Preferences>Sync. Disable automatic syncing and then restart EndNote.
  3. Make sure the Trash is empty both in EndNote online as well as in EndNote desktop. For EndNote online, Log into your EndNote online account, delete all references and all groups from EndNote online.
  4. In EndNote desktop, open the copy of the library you intend to work with going forward (this doesn’t have to be the backup). Open EndNote>Edit>Preferences>Sync. Add the following text to the end of your email address in the login field: 
    This is Case Sensitive.
  5. Click OK to close the preferences, and then click the Sync button.
  6. EndNote will then appear to authenticate and return the prompt: “A Sync library can be linked to only one account. Do not proceed unless you intend to break the link to the original account.” This happens because we tricked EndNote into thinking it authenticated against another user. Click OK, and EndNote will purge any knowledge of a previous sync.
  7. EndNote will then display a message, “Your local sync state has been reset. Please re-enter your E-Mail Address, restart EndNote, and sync again.” Click Ok.
  8. Close EndNote and open it again. Close all libraries then open the library which you would like to sync with EndNote online.
  9. Again go to sync preferences; enter the correct username/password and then sync. 
  10. When you next sync, you will get “A Sync library can be linked to only one account. Do not proceed unless you intend to break the link to the original account.” Click OK.
  11. You will be prompted to make a backup, you don't have to do this as you already have one.
  12. A complete sync will then begin. 
    The first full sync can take a significant amount of time, especially if you have a large library. Time taken to sync depends upon the size of the PDF attachments and number of references in the library.
    Once the sync is complete, login to EndNote online account and check whether you have the same set of references.

Find Full Text tries to retrieve the fulltext of articles in your EndNote Library.

Configure Find Full Text

Find Full Text is configured by default in the University's installer. If you find that the settings are missing, do the following:

Go to Edit > Preferences (on a Mac,EndNote > Preferences) and select Find Full Text.

OpenURL Path for easy copy and pasting:

Please leave the Authenticate with URL box blank. If you are not working in the biomedical area, you can uncheck the PubMed Linkout box to speed up Find Full Text.

Run Find Full Text

  1. Select the References in your Library for which you want the full text.
  2. Go to References > Find Full Text > Find Full Text....
  3. If you are prompted to Login to eResources, do so. Click the Continue button, and Find Full Text will start.
  4. Click to expand the Find Full Text heading in the EndNote left-hand menu, to see how many PDFs are being retrieved.

Full text will be retrieved for only some of the articles which you can access electronically. These factors will help:

  • Download your references from PubMed: If you have downloaded the references using the PubMed connection file, they will have links in the URL field which connect to the PubMed record on the web. EndNote can make use of the LinkOut links from PubMed to locate full text of articles.
  • Download your references from Web of Knowledge: If you have exported the references from the Web of Knowledge databases, they will have links in the URL field which connect to the Web of Knowledge record on the web. EndNote can make use of the Full Text links in Web of Knowledge to locate the full text of articles.
  • Use your EndNote Web account: Set up an account in Web of Knowledge and use EndNote Web in conjunction with EndNote to aid in full text retrieval. Note that you should enter your EndNote Web username and password in the EndNote Preferences.
  • Digital Object Identifier (DOI): If the record has a correct digital object identifier in the DOI field, EndNote can use that to locate full text of articles. ISSN - an ISSN in your citation will also help.
  • More tips from EndNote

  1. Open the Preferences menu in Endnote
  2. Click on Find Full Text
  3. Deselect Automatically invoke Find Full Text on newly imported references
  4. Click Save

  1. Open the Word document that contains references that were inserted using Endnote (these are the ones that show grey highlighting when you click on them)
  2. Click on the Endnote toolbar
  3. Click on Export to Endnote
  4. Choose Export travelling library
  5. You will see a message giving you the option to add to an existing Endnote library or create a new one. Choose your preferred option

One of the most consistent causes of Endnote errors is out-of-date software. Often this comes from a concern about losing data, or rumours that updated software has compatibility issues.
Actually, software updates are designed to stay ahead of compatibility issues - particularly with Microsoft Office365 issuing more regular and smaller feature releases rather than giant updates. Software updates address security vulnerabilities, software bugs, and add new features over time. The easiest way to manage this is to switch on automatic updating - whether that is for MacOS, Microsoft Office, or Windows.

There's usually a big annual software update for some platforms, for example Apple's most recent update for MacOS called Mojave which replaces the previous High Sierra. Endnote also has (roughly) annual updates, for example X9 is a new upgrade to X8. These kinds of big updates can't be automatically scheduled, and users need to kind of 'opt-in' by requesting the update. This is worth doing.

In the past, advice has been to uninstall the old Endnote before upgrading to the new version, but this isn't essential. To ensure the safety and compatibility of Endnote Libraries (especially if they aren't backed up online), we recommend installing the new software, checking that everything works fine, and then uninstalling the old software to keep the system clean. Of course you can create a backup of your Endnote Library before doing this if you wish, just to be safe.
Most compatibility bugs in Endnote can be resolved with a software update.


If EndNote doesn't work properly in the first instance, check the Clarivate Support page.

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