How to Create, Extract, and Manage PDF Annotations and Highlights

An efficient workflow for annotating PDFs, extracting highlights and comments, and filing them is essential for research, writing, and studying. Ideally highlights and comments should contain back-links that take you right back to the correct page in the PDF source document.Extracted-PDF-Annotations

Adobe’s Acrobat Reader DC, PDF-XChange Editor, and various other PDF readers allow you to annotate PDF files. But, you don’t want these annotations to remain “imprisoned” in your PDF. Your highlights and comments become a lot more useful if you can extract them, aggregate markups from several documents, and re-find them when you need them. Unsurprisingly, the free version of Acrobat Reader doesn’t allow the export of annotations as a word or text file.

To accomplish this in an elegant way, I recommend that you manage your PDF documents in Zotero, a free, open-source research document management system created and maintained by the Roy Rosenzweig Center for History and New Media     (George Mason University). With Zotero, you can collect and organize a large variety of document types, including PDF documents and web pages with the click of a few buttons.
To extract and manage PDF annotations in Zotero, you additionally need the free add-on Zotfile from Zotfile was created by Joscha Legewie, a professor at New York University. A big thank you to Dr. Legewie for programming and maintaining this excellent cannot-live-without add-on!

Adobe’s free Acrobat Reader DC is the most popular PDF reader; it is available on all major platforms, and allows you to highlight and annotate PDF documents. Consequently, in this post I am focusing on Acrobat Reader DC.

You can, however, use any PDF reader that includes annotating tools. My personal favorite on Windows PCs is PDF-XChange Editor (formerly Viewer), which does allow text export of annotations, albeit in a less ideal form.

As a PDf sample, I have added the free psychology text book by Openstax College to Zotero.1, 2 This is a massive 750-page book, so it serves as a good test case:


Double-clicking the book title opens the PDF file in Acrobat Reader (or your default PDF viewer). In the following screenshot, I have highlighted a passage and added a comment:

Adobe Acrobat Reader PDF annotationsSaving PDF highlights and comments

After I am done with annotating, I save the file back to Zotero, i.e., modify the original book: File->Save brings up this dialog:

PDF-annotation-save-dialogUpon saving the file I confirm that I want to overwrite the original file.

Troubleshooting Acrobat Reader DC – how to find and and overwrite a file in its original folder

Previous versions of Acrobat Reader automatically opened the PDF source folder and allowed the user to save the modified PDF document back to its original location, i.e., overwrite the file. If you have trouble saving your file, or are not been taken back to the source folder, you might have to change a setting to re-enable this behavior.3 In Acrobat Reader go to Edit->Preferences and deselect “Show online storage when saving files”:

Troubleshooting-Adober-Reader-finding-overwriting-PDFSave your settings, restart Acrobat Reader, and everything should work smoothly.

Extracting and managing PDF annotations

Back to our Zotero / Zotfile workflow: right-click the modified PDF attachment and select Manage Attachments->Extract Annotations:Zotero-Zotfile-PDF-extract-annotationsZotfile goes to work and inserts a note with the extracted annotations:

Zotfile-PDF-extracted-annotationsDouble-click this note to show the annotations:

Zotero-extracted-PDF-annotationsFrom the extracted-annotations window, you can directly copy your annotations and paste them into your favorite word processor.

Each annotation also contains a link back to the PDF file in Zotero, together with the page number. Clicking on this link takes your right back to the page where the annotation can be found:

Zotero-PDF-annotations-link-to-source-pageUnfortunately, in Acrobat Reader this only takes you to the right page if the file is not yet open. (In PDF-XChange Viewer, this function also works with currently open files.) If this bothers you, on Windows definitely give PDF-XChange Viewer or its successor PDF-XChange Editor a try.4 The free version might be all you need.

Aggregating annotations from multiple PDF documents

Alternatively, you can also select multiple documents (Ctrl+mouse) and aggregate all selected annotations in one report (Right-click->Generate Report from items):Aggregating-PDF-highlights-commentsThe report can be saved as a web page (e.g., back to Zotero) or copied to Word / your favorite writing software:

Zotero-Report-Aggregated-PDF-Highlights-CommentsIs setting up Zotero and Zotfile worth the effort if you only want to export annotations? If you are regularly annotating PDFs, my answer is a clear Yes! The time savings for managing and finding your annotations will easily compensate for the initial setup effort.

In a future post, we are going to look at including iPads and Androids in the workflow and other options for extracting highlights and comments from PDF documents.

This concludes part 1 of creating, extracting and managing PDF annotations. I hope you have found it useful. Have a great day!


  1. “About OpenStax College,” OpenStax College, accessed April 18, 2016, OpenStax College is an initiative of Rice University, providing a great selection of free, peer-reviewed college-level text books.
  2. Rose M Spielman et al., Psychology (OpenStax College, 2014),
  3. Richil, “‘save As’ pop up Box Does Not Allow Me to Save the Document.,” accessed April 18, 2016, Hat tip to Richil for finding this elegant solution.
  4. Tracker Software, “Tracker Software Products :: PDF-XChange Editor,” accessed April 20, 2016, PDF-XChange Editor has superseded PDF-XChange Viewer. If you want the free version, download PDF-XChange Editor standard. The setup includes the option to install the free version, which includes the annotation tools.

3 thoughts on “How to Create, Extract, and Manage PDF Annotations and Highlights

  1. Hi Helmut,
    your post seems to imply that you manage to link to a zotero/zotFile attachement using the links generated by zotFile after you copied the aggregated notes into your word processor (or whatever tool you use to take & manage notes / write)… how do you get that to work ?

  2. Hello Philippe,

    After extracting the annotations with Zotfile, Zotfile attaches a note that should contain the links to the pdf attachment.

    If you paste such a note into OneNote, Evernote, or Word, the pasted text should contain the annotations including links back to the pdf and page number.

    The links look like this: “zotero://open-pdf/2134802_HBKWFBBA/6”

    Clicking such a link should open the pdf via Zotero and jump to the page where the annotation is located (here page number 6). Word/OneNote might give you a security warning first, but allow you to override it.

    Make sure you don’t paste the note as text only. This would remove the links from the pasted note.

    Alternatively, Zotero itself is not too shabby for taking and aggregating notes. You could select multiple items and then generate a report from them (right-click->Generate Report from Items…). This would include the annotations as well.

    All the best.

  3. Hi Helmut, I had the same question as Philippe, and followed the instructions in your reply to his comment.

    But once I paste the note into Word, clicking the link only opens up Zotero, then nothing happens — it doesn’t open the PDF or display the page. Any idea why this is happening?

    I’m new to Zotero, so if you could point me in the right direction, that would be much appreciated!


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