Convert EndNote database to BibTeX

Once in a while I need to convert an EndNote library to a BibTeX library. For some reason this is much more difficult than it needs to be, and I always forget about how it c/should be done. I thought I wrote a blog entry about this the last time I struggled with it, but since I couldn’t find it I decided to write it up once again.

The process is based on using EndNote X2 on OSX and converting to a BibTeX file using the excellent free Bibdesk bibliography manager.

Open EndNote and Select the BibTeX export in Endnote

There is a BibTeX export template in EndNote, but for some strange reason this does not output a valid BibTeX file. However, to make things easier for ourselves, we will start from this template. If you don’t want to do these steps yourselves, you can download and see if the file I have created works for you.

Open the edit pane for the BibTeX style export

What we want to do is to tweak the template file, and this can be done by opening the template editor in EndNote (it would have been much easier to do this in a text editor, but the EndNote templates are stored as binary files…).

Open the template part in the edit pane

In the editor, find the “Templates” part.

Edit the template

1. Remove “label,” in the first line.
2. If you have written “research notes” in EndNote and want to use them with BibDesk, you need to add those to the template, by adding a line for “annote”.
3. Save the template and go back to EndNote.

Export the library

From the “File” menu, select export library. It should be exported as a text document using your altered BibTeX style. Unhook the “export selected references” option to export the entire library.

Rename the library to .bib

The file exported from EndNote is called .txt and should be renamed to .bib before being imported into BibDesk.

Import the library in BibDesk

Use the “open using temporary cite keys” to open the exported library. This is the trick to make it work, since we removed the labels when exporting the file from EndNote.

Ignore error messages

You will most likely run into some parse problems, but just klick “keep going” to ignore these.

Generate new cite keys

It is better to let BibDesk generate new cite keys for you, to avoid any further problems.

That’s it

Now it is probably time to check that nothing was last along the way.

Published by


Alexander Refsum Jensenius is a music researcher and research musician living in Oslo, Norway.

10 thoughts on “Convert EndNote database to BibTeX”

  1. Thanks Alexander for this. This was an incredibly helpful guide – especially the bit about not losing your research notes. You have been an amazing help – Michael

    minor edit: In last line change last to lost along the way.

  2. Many thanks for your guide.

    It helped me to export a large Endnote X6 database to BibTeX for use in BibDesk.

    Kindest regards,


  3. Thanks for the very well explained guide. everything went as expected, up till “Generate new cite keys”. this message did not display, instead got error message saying:

    File untitled syntax error line 113 (appears to be the last line) at end of input, expected “@”

    any suggestions?

  4. my mistake! I removed the entire first line in the template, including the @ symbol, instead of just the word “lable”. it worked perfectly…. again, many thanks

  5. Hello Alexander,

    When I click ‘Keep Going’, an empty library comes up. The ‘Generate’ cite key did not pop up. What is wrong?

    Below is the EndNote export setting:

    |   `author = `{Author},
    |   `title = `{Title},
    |   `journal = `{Journal},
    |   `volume = `{Volume},
    |   `number = `{Issue},
    |   `pages = `{Pages},
    |   `keywords = `{Keywords},
    |   `year = `{Year}

    And this is the exported file:

    author = {Ali Sid Ahmed M. Ali , Maarten L. P. Dirkx , Marcel G. J. Breuers and Ben J. M. Heijmen},
    title = {Inclusion of the treatment couch in portal dose image prediction for high precision EPID dosimetry},
    journal = {Medical Physics},
    volume = {38},
    number = {1},
    pages = {377-81},
    keywords = {*Electrical Equipment and Supplies
    Lung/ra [Radiography]
    Phantoms, Imaging
    *Radiometry/is [Instrumentation]
    Reproducibility of Results
    Tomography, X-Ray Computed},
    year = {2011}

Comments are closed.