Synchronizing EndNote between 2 computers via EndNote Web


As I have 2 computers, I’m very interested in the “sync” function of the last version of EndNote.  I’ve just created an EndNote Web account, and have synchronised it with my EN desktop library.

I tried to modify my references in my desktop version of EndNote on my 1st computer, then synchronize it with EN Web, and finally synchronize it with my library on my 2nd computer, hoping that the changes would be correctly imported. However, EN Web doesn’t recognize my library when I switch from one computer to the other, and duplicates every group and every reference in order to “fuse” the libraries.

What can I do to avoid that kind of problem? Thank you in advance for your answers.

We have a training video at that describes what needs to be done to synchronize a library between multiple computers…

Thank you very much!

That video is set to private. How do I watch it?

revised  (again)  Now at

but if it happens again - try finding the new one here

One of the Key things to remember when syncing is you sync one library to EndNote Web and back. If you go to a new computer and want to setup sync, you want to open a blank library and sync that to EndNote Web to get your references- if you open a copy of the original library on the new comptuer you get the duplication.

Colin Gillies

Technical Sup Rep RS

Thomson Reuters

Phone: +1 800-336-4474

Thank you for this tip about syncing two computers. I have been pulling my hair out because I am working on 3 different computers, and it keeps duplicating all the references. Now I know how to stop this from happening, and will give it a try! 

So does this mean that syncing across two computers, via EndNote web, is not viable day-to-day? I’ll give you an example:

During the day, I’m on my work machine and come across 5 new references that I add to my library and sync to EndNote web. When I go home, and pull up EndNote on my home machine (2nd computer), I’d like to sync so that those 5 new references are uploaded to this machine.

What is the best process for this? Would I need to open a blank library and sync from EndNote web any time I want to sync if I want to avoid duplicates? 

I understand the process to initially get set up for two computers, but what is the protocol for moving forward?


Once the initial Sync is established on the second computer through a new blank library, you do not need to follow that procedure again. You simply open the library you have synchronized previously on the second computer and click to Sync again to update it based on the information available on EndNote Web.

  1. Add the references to your work machine.

  2. Sync with EndNote Web.

  3. Go home and open your library. (The one you initially set up for your home computer.)

  4. Sync from your home computer to update the library.

This would update your home computer to add the records you previously added to the Web or any other changes you made. I hope this helps.

Jason Berman
Technical Sup Rep RS

Thomson Reuters

Phone: +1 800-336-4474

There seems to be a much easier way to sync between two computers. I did the following:

  1. Sync library on first computer to EndNote Web

  2. Go to File Menu and select “Compressed Library”  after several minutes, a compressed .enlx file is created.

  3. Copy the compressed .enlx file to the second computer (via flash drive etc.)

  4. Open the compressed file on the second computer in EndNote. It will take some time and will extract the library file and associated data folder (containing PDFs, etc.)

  5. Click Sync and enter account info.

By doing this, I saved much time and effort compared with the complicated steps shown in the YouTube video. The procedure does not cause any duplications. I think the issue with duplications occurs when you save a “copy” of the library instead of a compressed version of the original library.


Does anyone have a solution to work on a signle paper on these two or more computers (whether using dropbox or any other cloud system) once all libraires are synced, since the record number would differs form one libraires to the other?


I am interested in that as well. Because I use a program that gives me a lot of flexibility in drafting, but isn’t integrated with endnote, I just put all my references in with braces for later conversion in Word, e.g. {Schneider, 2013 #1404}, so reference numbers have to be the same. 

I compress it into an .enlx file and move it to the cloud or dropbox and take it out of the drop box and open it in a folder on the new computer.  then they are exactly the same with the exact same numbers.  I think those can then be synced and it will maintain the same numbers… but I don’t tend to do that. 

I totally with chrisdcallen. Just make your .enlx library and open that on the second computer. Then enable sync and its done!! EASY! All the groups, smart groups and group sets, and other bits and bobs are retained. You really do not need to go through deleting groups and making copies whatsoever…

Cheers! Petr

My sync is totally messed up now.

  1. I have one original home-computer library that I synced to web. That worked.

  2. When syncing with a new work-computer library, it emptied the web. I probably did something wrong there. (I think I copied the original library, opened it on my work computer, and deleted the data, so i had only the folders left)

Now, when I sync my home library, web stays empty, (only the folders are still there), the home library stays as it is.

When I sync a copy of that library from my work-computer it syncs with web and empties itself, instead of merging.

I dont know how to reset web, to start over again. I think thats what I need.

I am thankful for advice!

by the way: Is there anything wrong with simply using the very same library file on dropbox and access it from mac and windows? It seems like the most convenient option!

I think good re-set instructions are here.  Back up both the .enl and the .DATA folder and Folders (should also compress library to .enlx from File menu).  put those in a safe place.  From the machine with your library – start over with the instructions. 

Drop box has size constraints – and no way to properly lock the database files, so if two people access it at the same time or you leave endnote open on one machine and then go to the other machine and open it, you will corrupt the library.

However, you can put the compressed library there, and move it to and open it on the new machine and then perform the sync the first time and I believe it will be “synced” already and you can go from there.  

Hi, Just wondering if I can get some help/ advice please? I have been using Endnote on my Windows pc which is sync to the endnote web. I recently purchased a Mac and installed Endnote onto it. I have sync it and it has got all the data which were present on my web account at the time. I have since added more reference to my PC (original computer) and tried ot sync my Mac (second computer) but the new additions/ changes do not come across. I have checked my account on the and all the new references are there. But somehow I can sync them onto my (new) Mac. Any advice you can give me please?

thank you bro…

of course you can watch

have just done the same and got all my entries duplicated . DO we have to open a new library? Also how do we get rid of the duplications? delete them them individually?