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Step-by-step guide to using EndNote with LaTeX and BibTeX

I wrote this guide because I had many references in EndNote that I wanted to use in my LaTeX documents. I had to figure all this out the hard way — by lots of trial and error, if you follow this guide it should be easy for you. There are a few points to make: I have used every EndNote version since 4, but when I did my thesis I used version 9. This guide should work for other versions, unless Endnote have drastically changed something. I also use MikTeX and WinEdt on Windows. I don't have a clue about other configurations but they should still work with this guide.

In LaTeX use natbib. It is by far the best referencing package. Put ''\usepackage{natbib}'' in your header. Then in your document where you want the Bibliograpy to appear add:

\bibliography{name of your bib file}

I find plainnat pretty ugly so I wrote a better one bevbib4 you can use this, or write your own with custombib. Note that you don't type in the file name extension in the LaTeX document. For all this to work you need a unique ID for every paper you cite, it is best to be consistent and keep it simple, for example my unique ID for one of my papers is Weir04. This will print out as (Weir et al., 2004) [depending on the style used of course]. Your entries in your bib file should look like this:

Author = {Weir, B. S. and Turner, S. J. and Silvester, W. B. and Park, D.-C. and Young, J. M.},
Title = {Unexpectedly diverse \emph{Mesorhizobium} strains and \emph{Rhizobium leguminosarum} nodulate native legume genera of New Zealand, while introduced legume weeds are nodulated by \emph{Bradyrhizobium} species},
Journal = {Applied and Environmental Microbiology},
Volume = {70},
Number = {10},
Pages = {5980-5987},
Year = {2004} }

Now the guide begins. I assume you have an EndNote database (*.enl), back this up before continuing.

Preparing EndNote

  • To use my file "BibTeX_Export-custom.ens" you need to make these changes below. Or you can use the default file "BibTeX_Export.ens" (that I have made a couple of changes to) but you will need to use the "Label" field to type your unique ID. This may conflict with some websites that export references.
  • In EndNote go to: Edit -> Preferences -> Reference types.
  • For each type of reference you use click "modify reference types" scroll down and add "BibTeX" under the "custom 1" field. (don't do this bit if you are using the "Label" version).
  • Go to "display fields" and make Column 4 to display "Custom1" give it the title "BibTeX" (if you are using the Label version make the Column show "Label").
  • Go back to view your library. When you edit a reference by double clicking, a new field will appear (near the bottom) called "BibTeX" (or "Label"). In this field you type the unique ID (i.e. Weir04). Alternatively if you have a huge database you could use "Jabref" to automatically add these to your final BibTeX database. This software is also generally useful for managing your data once in BibTeX format.

Export the file as a BibTeX (*.bib) database

  1. Get my export filter style (Label version) or export filter style (Custom1 version) and save in the "Styles" directory of EndNote. Then select that file using the style manager in: Edit -> Output Styles. Make sure this style is selected in the main view window.
  2. Go to: File -> Export. Save the file as a text (*.txt) file. Move this file to your LaTeX directory you are working with and rename to a *.bib file.
  3. Now when you cite a reference use the command \citep{Weir04} or \citet{Weir04} to get a parenthesis or text citation respectively (just try it out to see what happens).
  4. Run LaTeX or pdfTeX on your file twice then run bibtex then LaTeX or pdfTeX again a few times. Repeat if required. Or just use Texify. You should only have to run BibTeX again if you make a new *.bib file.
  5. With some luck the citation should be inserted and referenced at the end.

The fiddly bit is going back to those references and using proper LaTeX commands where necessary i.e. using \emph{Species name} (type this into the EndNote field) . This will of course look like rubbish if you use the same EndNote database for MS Word documents. I keep two databases.

Notes on using the Style file

  • For electronic references I used the "book" reference type, and in the notes field add the url in this form: "URL: \url{}" . Yes this is a hack. The note field in other reference types will not be used (see below).
  • When you add authors make sure they are in this format: "Sandberg, A. M." note the spaces, this is important. You can use full names (see below), but again: spaces.
  • Don't worry about en-dashes in the page ranges, this is taken care of automatically.
Author = {Irwin, Geoff and Walrond, Carl},
Title = {When was New Zealand first settled?},
Publisher = {Ministry for Culture and Heritage},
Address = {Wellington},
Series = {Te Ara -- The Encyclopedia of New Zealand},
Note = {URL: \url{}},
Year = {2005} }

EndNote Export was not listed on your Output Styles menu?

If "EndNote Export" is not listed in the Edit -> Output Styles menu:

  • Select Open Style Manager.
  • Find the "EndNote Export" style and check it ON. Close this window.
  • Make sure that "EndNote Export" is now checked in the Edit -> Output Styles menu.
  • Select the references you want to transfer.
  • Choose File -> Export. Make sure you are exporting the references as Text file Only, then click on OK.

Thanks to Nora Lieske for this tip.

Other Websites

The information on this page may not be exactly what you are looking for, some other websites which might be of help are:


Weir, B.S. (2012) Step-by-step guide to using EndNote with LaTeX and BibTeX. NZ Rhizobia website.