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Working with PDFs in EndNote

Import PDF(s)

EndNote can import and create records from PDF files. EndNote can also import PDFs from sub-folders, and is able to create a group set for the imported files.

To import PDFs into your EndNote library:

  1. Select File> Import> File
  2. At the Import File text box, click on Choose, to select a PDF
  3. At the Import Option text box, select PDF from the drop-down menu, then Import
  4. Your selected file will be imported with PDF file attached to the reference

  • With EndNote X7 and later versions, you can leave the Duplicates option set to Import All because EndNote will try to identify existing records in the library that matche the PDF. If it identifies a match, it will attach the PDF to the existing record instead of creating a new record.

N.B. If your imported PDF has a DOI: it will import with quite a few of the fields filled in.
        If your PDF does not have a DOI: it will create a blank record with the title of the reference the name of the PDF.

Import PDFs as a group set

To import PDFs into your EndNote library as a group set:

  1. Select File> Import> Folder
  2. Choose the folder that contains subfolders of PDFs
  3. Tick the boxes for Include files in subfolders and Create a Group Set for this import
  4. Click Import

Find full-text PDFs

EndNote has the ability to search for full-text PDFs of journal articles that have already been added to your EndNote library.

  1. Highlight the reference(s) you'd like EndNote to find the full-text
  2. Go to References menu > Find Full Text > Find Full Text or click on

3. You may be prompted to enter your Deakin username and password. Enter your Deakin credentials and click Login. Then click Continue

4. Click OK to agree to the copyright usage notice

5. When EndNote completes the search, you will see how many full text articles were retrieved on the left side of the window. The retrieved PDFs will be attached to their respective reference and can be viewed in the Attached PDFs tab.

N.B. There are some important limitations to bear in mind when using EndNote's Find Full Text feature.

  1. EndNote is unlikely to retrieve all PDF files.
    • In many cases, you will be required to download the PDF separately and manually attach it to the reference in your EndNote library.
  2. The search process takes quite some time and freezes the program, so only select up to 10 references at a time.
  3. Articles in the ScienceDirect database, published by Elsevier, cannot reliably be identified using Find Full Text.
    • This is a known issue, and is awaiting for a fix from EndNote's developer, Clarivate. PDF files from ScienceDirect therefore need to be manually downloaded and attached to references in your EndNote library.

Manually attach a PDF

To manually attach full-text PDFs to references in your EndNote library:

  1. Download the PDF file and save it on your computer
  2. In EndNote select the reference in the central window/list
  3. Click on the paperclip symbol above the record
  4. Select the PDF file you want to attach from your computer
  5. Click Open

PDF viewer

To open PDF files in a full window view:

  1. Highlight the reference in EndNote central window/list
  2. Click on PDF viewer panel
  3. Click on Open PDF icon

N.B. EndNote will automatically open the first PDF attached to a reference when you select the PDF viewer panel.

Now you can annotate PDF files attached to the reference. These annotations are also searchable in EndNote.

Mac users:

  • Users may encounter problems with the EndNote PDF viewer.
    • Clarivate advises that this can affect users on any of the Mojave, High Sierra, or Sierra operating systems. Clarivate recommends annotating PDFs in an external PDF application or using the free EndNote for iPad app.

PDF auto renaming

EndNote has a feature that will rename PDFs automatically as you import them into EndNote

  1. Select Edit menu > Preferences
  2. Select PDF Handling
  3. In PDF Auto Renaming Options select the naming format you want or customise your own format
  4. Click OK

PDF auto import folder

You can nominate in EndNote a particular folder where you like to download your PDFs. When you nominate a folder, EndNote will monitor this folder, and automatically import new PDFs added to this folder into your EndNote library whenever you open your library.

  1. Select Edit > preferences
  2. Select PDF Handling
  3. Under PDF Auto Import Folder tick the box next to Enable automatic importing
  4. Select the folder you want to be scanned regularly
  5. Click OK

N.B. EndNote creates a folder called imported within your nominated folder and automatically moves all the PDFs that it has already scanned into this folder. This ensures that EndNote won't scan the same PDFs again.

Find full-text PDFs with Kopernio

Please note that as of late August 2019, Kopernio is no longer working with Google Scholar.

The problem seems to be connected to Google Scholar's terms of service (there is relevant information at this Kopernio support ticket). Kopernio still works with other research sites (e.g. Web of Science), but the lack of availability for Google Scholar will reduce Kopernio's relevance for some users.


Kopernio is a free browser plugin that:

  • identifies published PDF versions of academic articles while you browse research sites (e.g. Web of Science).
  • provides a cloud storage "Locker" for storing and sharing PDF articles
  • enables RIS reference files to be downloaded for importing into EndNote

Kopernio is presently available for Chrome, Firefox and Opera. It is closely integrated with Web of Science but also works across other research sites, depending on your home library's subscriptions.

Further general information is available from the Kopernio website, including the detailed FAQ here.

Kopernio has met with both enthusiastic responses (e.g. this report in Nature) and scepticism (e.g. this piece in The Scholarly Kitchen).

Kopernio at Deakin

Kopernio publishes library-specific how-to guides. See here for the Deakin guide.

There is also a general online guide published by Clarivate which includes a hands-on video demonstrating how to install and start using Kopernio.

If you want to share articles using the Kopernio Locker, be aware that you must not share articles from subscription journals in breach of Deakin's licence obligations. You can read more about sharing articles from subscription journals here. 

Delete / Disable Kopernio

You cannot delete your Kopernio account yourself. You must email an account deletion request to

To disable or remove Kopernio from your browser, you need to access your browser extensions. In Firefox, for example,

  1. Select Add-ons from the main drop-down menu (the lines on the top right of screen).
  2. The Kopernio plug-in should appear in the on-screen list. Choose either Disable or Remove.

To permanently delete a PDF from your Kopernio Locker,

  1. Archive the PDF by selecting the small cross at the bottom right of the PDF icon
  2. Access the Archive from the menu on the left of screen and click the trash can icon below the PDF