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EndNote desktop: self-paced learning

EndNote Sync - backup and synchronisation in one

Why use the EndNote Sync feature

The EndNote Sync feature creates and uses an account with EndNote Web, a simplified online version of EndNote.

It has two main advantages:

  • Your references are backed up, and can be recovered if your local library is lost or corrupted
  • You can synchronise your references between two computers, e.g. a work computer and a home computer
From the Edit menu, select Preferences.

In the Preferences dialog:

  • select Sync
  • Click the Enable Sync button
screenshot showing Preferences dialog with Sync option selected, indicating location of Enable Sync button

If you do not already have an EndNote Web account, click the Sign Up button.

If you do have an EndNote Web account, you can enter your login details to sync with your existing account (references from your desktop and web libraries will be merged).

screensot of the EndNote login, indicating Sign Up button

If you are signing up for the first time:

Enter your email (twice, to check for spelling errors), and click the Submit button.

Fill in all fields on the next page that are marked with a red asterisk (if you wish, enter the university address instead of your personal address). Scroll to the end and click the I Agree button.

EndNote online registration

Once you have completed the process, click on Done 

Click the OK button to close the Preferences dialog.

You may briefly see an Authorizing progress bar on your screen.

screenshot of completed Sync page in the Preferences dialog, indicating OK button

To sync for the first time, click the Library button.


You will be asked if you want to create a backup of your EndNote library.

For the sake of your valuable research data, the Library recommends you select Yes.

screenshot of dialog which suggests creating a backup file

Select a folder and filename for your backup.

If you add the date in reverse order (year month day) to the start of your filename, you can quickly sort backup files by filename in the future.

screenshot of save dialog for backup file, indicating date added to filename

The first sync may take considerable time, particularly if you have a lot of references with PDF (or other) attachments. Later sync sessions will only make incremental changes and will usually be faster.

You can check the progress of your sync by clicking on Sync Status.



Sync between two computers, e.g. home and work

  1. If you want to sync another computer to the same EndNote Library, first follow the instructions above for syncing the first computer with an online account.
  2. On the second computer, create a new empty library (File menu, New).
  3. As above, set up the same account:
    1. Edit menu, Preferences
    2. Sync tab, click the Enable Sync button
    3. Put in the same email address and password you used previously to create the account (do not register again)
    4. click OK, then OK again
  4. You can now use the Library menu and the Sync button to sync the online content with this new empty library, which will download all the online references.

After this, any time you click the Sync button on either computer, any new local changes on that computer will be uploaded, and any new changes found online will be downloaded. 

Note: new references in either the web version of the library or the the desktop version will be merged during a sync operation.

While EndNote will automatically sync every 15 minutes1 whenever you wish to sync manually2, click the Sync button near the top of the EndNote window.

1unless you un-tick the Sync Automatically checkbox in Preferences

2for example, once on your work computer at the end of the day, then again immediately as soon as you open up EndNote on your home computer