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An introduction to EndNote for Mac and Windows and EndNote Online.

Sync your EndNote Online and desktop libraries

Sync your EndNote Online and desktop libraries

You can sync your EndNote online and desktop libraries (including the attachments and figures).

When you run sync, the data in your EndNote desktop and EndNote online libraries are merged.

After the sync completes you will have identical groups and references in both EndNote Online and EndNote Desktop.

Important things to know about the sync process:


Before you try sync for the first time, make sure you back up your EndNote Library first.

Even if you sync your library with EndNote Online you should still regularly backup your EndNote Library

Sync works with only one EndNote desktop library and EndNote Online account at a time.

Syncing with EndNote Online includes all groups and group associations but group sets, smart groups, and combination groups will not be displayed in your online library.

The sync process includes ALL changes to references in either library. For example, if you delete a reference in either the desktop or online library and then sync, the reference will be deleted from BOTH libraries.

The first time you sync your library on another computer you should open a new, empty, EndNote Library and then sync. This will download all your references from EndNote Online into your library. From then on, when you sync on that computer, you do not need to open a new blank library.

Set your preferences

Set your preferences

To allow EndNote Desktop and Online to sync:

  1. In EndNote Desktop, go to Edit > Preferences (Windows), or EndNote X9 > Preferences (Mac).
  2. Select Sync
  3. Click the Enable Sync button.
  4. Enter the email address and password for your EndNote Online account.
  5. Click the OK or Save button.
  6. You may be prompted to enter your name, address and other details to complete the integration of your online and desktop accounts.
  7. Note: you can tick the Sync Automatically checkbox to have EndNote automatically run the sync process every 15 minutes in the background.

Sync your EndNote desktop and online libraries

Sync your EndNote desktop and online libraries

The sync process is always initiated from EndNote desktop.

Once you have set your preferences you simply need to click the Sync Library button in EndNote desktop.

For example in EndNote for Windows the sync button is next to the help button:

Troubleshooting Sync

Troubleshooting Sync

If you experience issues with Sync, make sure you:

  • Empty the trash before syncing.
  • Only sync with one EndNote library.

Also, if you are syncing on a different computer for the first time, open a new empty EndNote library and then sync to download all your references from EndNote Online. From then on, when you sync on that computer, you do not need to open a new blank library.

Sync Conflicts:

A Sync Conflict may occur if you edit a reference in both EndNote desktop and in EndNote online between Syncs, as EndNote does not know which change you want to keep.

If there are any conflicts, a Sync Conflicts group will appear:

Right click the group and select the Resolve Conflicts option. You can either keep the EndNote desktop reference or the EndNote Online reference (the version of the reference you do not choose to keep is permanently deleted). If you need to you can also edit either reference and keep that edited version.

Sync Status:

Double click Sync Status in the group area to view information on the last Sync operation, including any errors such as storage limit, authentication or internet connection errors.

Reset Sync

Reset Sync

There may be instances where the sync between EndNote Desktop and EndNote Online needs to be reset because the user:

  • may wish to sync a different desktop library with their online account

  • is experiencing issues too complex to troubleshoot

  • or simply wishes to start afresh

Prior to executing the steps below, please ensure you backup your EndNote Desktop Library using the Compressed Library function - see section "Compress Library for EndNote X and later users".

To reset the sync:

  1. Open your EndNote Desktop library and click on Edit ► Preferences Sync. Untick Sync Automatically and then restart EndNote.

  2. Delete all references from EndNote Online by selecting the All checkbox under All My References and then click Delete.

  3. Delete all groups from EndNote Online, with the exception of any Shared Groups or ResearcherID Groups that may be setup by clicking on Organize  Manage My Groups  Delete.

  4. Ensure the Trash in both EndNote Dekstop and EndNote Online is empty.

  5. In your EndNote Desktop library, click on Edit  Preferences  Sync and add #!resetLocalSync to the end of your email address

    • Note: This is case sensitive - #!resetLocalSync NOT #!resetlocalsync

    • e.g. if the email address was, change this to!resetLocalSync

  6. Click Apply and then OK.

  7. Click the Sync button.

  8. 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.” Click OK and another message will follow “Your local sync state has been reset. Please re-enter your E-Mail Address, restart EndNote, and sync again”. Click OK.

  9. Go to Edit ► Preferences Sync and remove #!resetLocalSync from your email if you wish to sync your existing library.

    • If you wish sync another library, open the library and click on the Sync icon in EndNote Desktop to commence the syncing process. You will once again receive the following message “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 and you will be prompted to make a backup. Click Yes and follow the prompts do so since this is a different library.

  10. A complete sync will then begin.

EndNote Sync: EndNote X7.1 and Later

EndNote Sync: EndNote X7.1

Further help

Endnote for iPad and iPhone

Endnote for iPad and iPhone

Endnote of iOS allows you to easily view, edit, organise and share your references while you may be on the move. You can have your full library of references synced to your iOS device, desktop computers and online account.

The most recent version of Endnote for iPad is v.3.1 and last updated on 18 November 2020. It requires iOS 11.0.

  • It comes with its own built-in Web browser with links to Web of Science, PubMed, Google Scholar, and PLoS
  • It also offers improved PDF annotation features. 3rd party storage with OneDrive, Google Drive and Dropbox has been enhanced.

Download Endnote for iPad

Access a video to help you make the most of using Endnote for iPad.