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

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.

To sync you will need to:

Set your preferences

To allow EndNote Desktop and Online to sync:

  1. In EndNote Desktop, go to Edit > Preferences (Windows), or EndNote X7 > 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

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

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.

EndNote Sync: EndNote X7.1 and Later