Cannot add EndNote data files to a compressed folder Windows XP, 7 (and probably Vista)

When EndNote adds a data file (PDF) for some strange reason it creates a folder named with the PDF file name.


…\MyEndNotesLibrary.Data\PDF\Leverett_Testimony-“The Geopolitics of Oil And America’s International Standing”-2706297365

This creates the problem of long file path names in Windows.

But it creates another problem too, since although according to EndNote help:

“Note: In order to maintain cross-platform compatibility, any of the following characters in a filename will be replaced by an underscore when EndNote saves a copy of the file in the DATA\PDF folder with a relative path.”

But only a small number of such illegal characters are stripped out:

These characters are replaced with an underscore


(back slash)


(forward slash)






(question mark)


(quotation mark)


(less than)


(greater than)


(vertical bar)

In the above file path example, the “curly” quotes create a problem and you cannot add, for example, data file folders with those characters to a compressed folder.

There is only on way around this issue:

  1. save a copy of the attached PDF and rename it without using illegal characters

  2. delete the attachment from EndNote

  3. save the change

  4. re-add the re-named attachment to EndNote

  5. save the change

A very very painful process when you stumble upon this issue after happily accepting original file names for years!!

The problem could have been avoided if EndNote simply created a PDF foldername based on the underlying record ID for example (I guess in the above example, say …\PDF\ 2706297365_0001{filename stirpped of illegal chars}.pdf)

The developers try very hard to please everyone!  Many users requested they not change the PDF title used, but that can lead to problems such as you have encountered.  I, for one, like to be able to find my PDFs by the naming convention I used in the folders, so I can access them easily from outside Endnote as well, but it is very important to keep them short and sweet, due to Windows limitations on file name length (which includes folder names) and character restrictions. 

However, I can’t comment on the reasons behind their putting each PDF in a folder which compounds the problems. 

Creating folders to store attached PDFs based on a unique record identifier probably would have been a better design but is not the way we implemented this initially. The design was based on a system that was optimized for EndNote to most easily and quickly access these files internally.

We have looked into improving / updating the organization and naming conventions for attached files but all of the options seem very complex and time-consuming to implement and would have many backward compatibility issues.

We can research this further to see if there is something that we can improve at some point in the future.

Jason Rollins, the EndNote team