PDF attachments: why is endnote putting each PDF in an individual folder?


Just started working with Endnote X8 (Mac version) and have noticed that when importing PDFs Endonte is storing them each in an individual folder, i.e. a single PDF in a single randomly-named folder.  I’ve been through the preferences and can’t find a way to override this.  Given I have approx. 2000 references, surely each PDF is not going to reside in it’s own radomly-named folder - this is a completely nuts approach to digital file management.

I’ve previoulsly used Papers for Mac, which gives complete freedom to customise PDF attachements - by author; by journal; by year etc.  Can this be done in Endnote?

And another frustration - Endonote will not rename PDF’s based on the criteria I’ve set.  This seems more prevalent for PDFs for which I’ve needed to manually enter the reference information. 

If anyone can shed any light on my frustrations, I’ll be very grateful!!

Many thanks,


Hello Cain,

I’m sorry for the trouble you’re having with EndNote’s PDF indexing.

EndNote creates a unique folder to ensure that PDFs do not get overwritten by other PDFs.

And, unique folders containing the filenames is the route we’ve chosen to ensure this doesn’t happen.

In the EndNote Preferences, under PDF Handling, it is possible to adjust the convention by which EndNote automatically renames the relatively linked version of that file.

Otherwise, the best way to get a copy of the PDF attached to an EndNote reference is to highlight the record in the list, and under References - File Attachments, there is an option for “Save As…”, which will create a copy of the PDF attached to that record, and offer you the option to save it wherever you like.

Please let us know in the Suggestions forum if there is something you would like changed, or you think would be an improvement to the software.  We’re always looking for ways to make things better.



Hi Steve,

Thanks for your reply.

Unfortunately, in this case, Endnote’s file organising system isn’t going to work for me.  I need a file system that is logical, organised and useful outside of the software, as one day I may decided not to use Endnote or it may stop being developed etc. - having 2000 papers in 2000 randomly-named folders would be a nightmare to clean-up.

Many thanks again,


To each their own.  I have endnote to retrieve my PDFs and I can find them by a simple name year search because of my chosen naming convention in their relative location if I wanted to find them on the machine.  I don’t need them “physically” in one place, or manually organized.  Even before the option to attach PDFs (yes I am that old) my printed copies were (and the pre 2002 or so still are)  stored by record number in binders.  


It is a bit strange that with so many alternative solutions, endnote engineers opt for the awkward one folder-one file solution to prevent pdf file from being overwritten. Check out papers3  they solved it with an extremely flexible solution. Also, the naming of pdf is more flexible than in endnote.I am sure endnote software engineers can also excel! Rita

I am a long time EndNote User. Until now, I have been using EndNote in a Windows computer. Now I am using a Mac (macOS Sierra). I have now an EndNote version for Mac. 

My Problem:

Until now I had my Library.enl (with around 1500 entries) in a folder “D:/Literature”. In this folder were also all my PDFs.

I did not let EndNote rename or relocate my PDFs. I attached the files by drag and drop.

In the new computer, EndNote does not find the PDFs. 

My solutions (they did not work):

To solve the problem, I tried to convert the file attachments to relative links, in the end I had a folder with a strange name (a couple of numbers) for each PDF, about 1500 folders… That’s really not what I was looking for :confused:

I tried also to open the Library.enl file with a text editor. I tried changing all the paths by copy and paste. This did not work either.

My question:

How can I copy the Literature folder (the Library.enl and all PDFs are there) to the Mac so that the Library.enl finds the file attachments?

Thanks in advance for your help!


How does the mac deal with a newly attached absolute path?  I doubt that Endnote will ever change how they create the PDF locations for relative paths.  – The software would be so redesigned – they might as well give it a new name.  

Hi there! This is a bit late, but maybe it will help you and/or anybody else that is searching for similar solutions via Google.

>>> How can I copy the Literature folder (the Library.enl and all PDFs are there) to the Mac so that the Library.enl finds the file attachments?

I’m not sure about the associated .enl files for each PDF, but this is the method that I’ve used in the past to download all PDF’s in a library:

1. Instead of moving/copying each PDF in each individual folder, navigate to the folder with all of the folders (in your case: “__D:/Literature”).

2. In the file explorer/finder search box, enter *.pdf and press enter.

All of the library’s PDF files should appear where you can select them all and moving/copying them to wherever you need them. Best of luck!

Hello all, 

I also find it quite sad that there is an individual folder for each pdf, as I do not want to depend on EndNote for my library to work.

In my case, I am adding a unique ID number to each piece of literature and have chosen to have EndNote automatically rename them as ID-Author-Year. Hence, identical names and overwriting of files are prevented. One folder would be possible and way better.



PS: On the upside, here is a way to list those PDFs, copy them all and paste them into one folder (keeping the original structure for EndNote): libguides.uthsc.edu/c.php?g=320620&p=5253808

Yeah, I think the individual PDF folder thing is a requirement of the database structure they use.  

Not exactly a constraint of the database structure, but rather a design decision. For each attachment, there is a record in a table that contains the unique reference Id and a path to the file. The file path field could hold anything they wanted as long as the file name would have been unique (by appending the unique reference Id for example to the filename).

It is an odd design choice, one that I would have not made, but we have to live with it.