Saturday, March 21, 2009

Exporting References from Endnote to BibTeX

Endnote has a bibtex export style. I'm not sure why they bothered. It doesn't work, it's never worked and from the looks of things this and a couple other issues with Endnote are never going to work. The articles and third party software i've tried just don't work or are a real pain to impliment.

I use JabRef for my bibtex reference manager. They seem to be on top of it. Besides the ease of use and functionality of the software in the first place, they seem to have an easy and built-in (sort of) way to export correctly from Endnote.

Step 1
In JabRef click Tools-unpack Endnote Filter Set (this is a zip file so put it anywhere)

Step 2
Open the zip and read the "read me" file. It has instructions to go from Endnote to JabRef and JabRef to Endnote. For our purposes copy BibTeX Export to JabRef.ens and BibTeX Export to JabRef2.ens into the styles folder
(something like C:\Program Files (x86)\EndNote X2\Styles).

Step 3
In Endnote click on file-export. Then in Output Style, select Use Another Style. In the search box type jab and it'll bring up the two new styles. You can see the difference in the preview pane, but JabRef.ens is the one we want rather than JabRef2.ens.

Step 4
Save as a text file

Step 5
rename the file from .txt to .bib and open it in JabRef. You can also import. WARNING!! this will FAIL if any of the references has a bibtex key already that contains a space (or punctuation maybe too). Any key like this needs to be deleted or else it won't work.

Step 6
In JabRef, select all and click the magic wand to generate new keys for all entries. DONE

I actually exported some references from JabRef an copied all my Endnote exports into that file. There's some stuff in the JabRef export that is commented out. I don't think it needs them, but just incase.


Xotlatzin said...

Thank you so much Josh, your post is very useful!

Best regards,


gultepe.e said...

Thank you very much for this detailed post, it helped a lot.

Actually, I can say just learning that "EndNote export to BibTex" doesn't work was quite helpful information.


Ghad said...

After many frustrating hours I haven't been able to get this working. I followed your procedure, and having unpacked the styles and changed the export settings on EndnoteX2 etc, none of the references seem to make it to Jabref after opening the .bib file. I'm really not sure what is going on here, so any other tips or tricks?

Josh said...

It seems like there is a bunch of ways to do this conversion, but i'm not sure if any (including mine) is completely foolproof.

This site

has a bunch of methods listed at the bottom. It suggests that if it's not endnote version X2, my method might not work. I'm not sure about that because I'm thinking I originally did it with vers. X1.

Another method that might work can be found

At first glance, his method looks easier than the rest. I know the guy and I know this is how he always does it.

Ghad said...

For whatever reason, Endnote just won't export the appropriate Bibtex styles directly into a text document using Endnote itself. All you get is the linear list of authors, title, date, pages etc.
However, the appropriate Bibtex style seems to be retained if you first use the 'insert citation' feature in Word. You can then save that word doc as a text/.bib file and Jabref seems to have no problem importing that. Yes, I know this is hopelessly inelegant...

gultepe.e said...

For James:

Before trying this method, I had already downloaded "Endnote to Bibtex patch" from Endnote webpage. That might do the trick.
Best of luck,

Martin Uppman said...

Very nice, I finally got the references exported from Endnote to JabRef. The preview mode works fine, but there are just garbage in the "Author", "Title" in the reference list though. Have someone experienced this before?

Dan said...

Excellent! It took me literally no more than 15 minutes to figure out the whole process and to get it to work (using Endnote X2 and the first Jabref export style). Jabref's magic wand is a huge timesaver! Was dreading having to write all the labels/IDs myself.

Something else of note which is useful, is in the Jabref FAQ ( it tells you how to enable the bracing of all capitals in the title fields so that MikTex doesn't automatically make them lowercase.


Mr. Gunn said...

Mendeley can import Endnote XML and export BibTeX, so that should be pretty straightforward for anyone struggling with Endnote export.

isroi said...

I cannot find the zip endnote filter file. Where is the file located? thanks.

Josh said...

The Endnote filter set is found in the Jabref Tools menu "Unpack Endnote Filter set"

Emily said...

I seem to be having the same problem as isroi ... when I do "Unpack Endnote Filter set" in Jabref, it has me select a location to put the (unnamed) zip file. I do so, and type in a name, but then there is no zip file anywhere. I'm sure this is something dumb but I can't for the life of me figure it out. I'm using Mac OS X 10.6.6; just downloaded Jabref.

Josh said...

This seems to be a common problem in version 2.6. I can confirm that it no longer works on my computer either. I found the filter set for download at

Good luck!

Thomas Hefti said...


Barrie said...

Thanks, it worked perfectly.