How to annotate PDF files in Linux using Xournal

The Portable Document Format (PDF) has become the de facto standard for document distribution as it ensures that the distributed text and images can be read or printed appropriately under a variety of platforms. If I recall correctly, it must have been over 8-9 years since I had first searched the web for a PDF viewer that would offer basic PDF editing capabilities. Basic editing capabilities should be translated to providing the user with the ability to highlight, bookmark and take notes inside the PDF document. Of course, there are many high quality commercial PDF editors out there, but many users (including myself) believe that, since the PDF format has gained so much popularity, simple annotating capabilities, such as text highlighting, should be part of a free viewer’s core functionality.

There are many ways you can edit pdf files in Linux, but, the overwhelming majority of them includes lengthy procedures that just end up wasting your time. One program that has performed better than all the others I have tried so far is Xournal. Xournal is not actually a PDF annotator/editor. As the author states:

Xournal is an application for notetaking, sketching, keeping a journal using a stylus.

This software has not been designed for PDF annotation. This feature is simply a side-effect of xournal’s main function, which is notetaking using a stylus. Xournal makes the annotation of a pdf file possible by loading the document as an image and letting you use its sketching tools on a separate layer on top of that of the pdf document. It can finally merge the layers into a single one and save the document as an annotated PDF file, while preserving the original text.

Taking into account that PDF annotation is not Xournal’s purpose of existence, one could say that it does this job quite well. But in comparison to other professional PDF editors, it turns out that it is not as efficient. This is because xournal can only load the PDF document as an image. For instance, when the user tries to highlight a line of text, xournal cannot recognize the text boundaries and use them as a guide, so to help the user highlight that particular line with ease. The user still has to draw a perfect line on top of the actual line of text in order to highlight it.

I admit that when I first tried to highlight some text in a pdf document using xournal’s highlighter, I was deeply disappointed. But, as soon as I started exploring its configuration options both those that are available from within its graphical interface and those that can be directly edited inside the config file, I realized that it was easy to greatly improve the text highlighting experience.

The rest of the document has to do with configuring xournal in such a way that it is more convenient to use it to highlight text inside PDF files. Although some of these settings can be set from within xournal’s graphical interface, I recommend editing the configuration file directly: /home/gnot/.xournal/config, since it contains more options than those available in the GUI.

The ruler exists in order to make life easier when you highlight text. It is highly recommended that you enable it for text highlighting:


If highlighting text is your main use of xournal, then you can make it the startup tool as well.


The following options make xournal’s window to start maximized and set the initial zoom to 150% respectively.


The following options configure the highlighter. You can set the 3 pre-defined levels of thickness and which one will be the default one, set the default color and finally set the opacity (the default opacity level of 50% is just too much).



Noone said that annotating PDF files in Linux is an easy task. I have tried many open source tools for that job, but xournal seems to be the best one at the time of writing.

How to annotate PDF files in Linux using Xournal by George Notaras is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
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About George Notaras

George Notaras is the editor of the G-Loaded Journal, a technical blog about Free and Open-Source Software. George, among other things, is an enthusiast self-taught GNU/Linux system administrator. He has created this web site to share the IT knowledge and experience he has gained over the years with other people. George primarily uses CentOS and Fedora. He has also developed some open-source software projects in his spare time.

13 responses on “How to annotate PDF files in Linux using Xournal

  1. Geoff Permalink →

    Thanks for this article. I have also tried many open source options and have been universally disappointed.

  2. Geoff Permalink →

    Note that you have to click “Options > Save Preferences” for the config file to be created. Simply creating a file and copying the author’s tweaks did not work for me. I had to have the application make the config file, then edit the keys provided.

  3. deadlycheese Permalink →

    Oooh, very helpful, I’ve been looking for something like this forever.

    By the way, the version that is currently in the Fedora 9 repositories has most of your suggested configuration changes incorporated already. All I had to do was
    “smart install xournal” and I was good to go.

  4. brontosaurus Permalink →

    Thank you for this info!! I had tried 4 other programs that wouldn’t do what I wanted. This was perfect for marking up a PDF file I was proofreading for a colleague.

    One note, I’m using Ubuntu (Hardy) and the version accessible through the GUI Add/Remove program interface was not the newest version available and wouldn’t work for me (it was 0.4.1). After downloading and installing Xournal from its sourceforge site (version, it worked awesomely.

  5. londonlnx Permalink →

    This post is very useful for me. Thank you so much!

  6. Jenny Permalink →

    Thanks for tips!

    I’m using Xournal 0.45 and the ruler on startup is now split up by tool type, so:


    Cheers :)

  7. Joan Permalink →

    Thanks very much for the information. I plan to use xournal for my classes, and having the possibility of annotating pdf files was the last thing I needed to be able to do everything from a laptop.

    Best regards.

  8. Chris Permalink →

    I wish the highlighter mode in xournal would give you the option of having the highlighter color not affect or “bleed” into the text foreground color, just the background color. Highlighting text in office word for example does this where the text foreground color (usually black) does not change but the background color takes on the highlighted color. This makes the highlighted text more readable.

  9. Viktor Permalink →

    Agreeing with Chris, this program sucks. Have been using pdf annotator in windows and trying to find a replacement. Highlighting your text should make it easier to read, not fuck up your eyes.

  10. George Notaras Post authorPermalink →

    @Chris & @ Viktor: Hi. As I explain in the post above, xournal has not been designed for PDF highlighting. I don’t consider it the best solution for PDF highlighting, but I don’t think you can find any other free software that does it well.

    As for closed source software, the latest Adobe Reader X supports highlighting and comments on the pdf file. Also, Foxit pdf reader has supported this feature since a few years.

  11. Bob Permalink →

    What are the steps?

    I started a New Layer, highlighted it and saved it as a file separate from the original PDF. The saved file was filename.pdf.xoj. When I try to Export to PDF I get a plain text file but NO PDF file is created.

    How do I merge the layer of my highlighting and export the result as a PDF file; how do I save “. . . an annotated PDF file?”

    Please list the steps.

  12. Sweet Sorrow Permalink →

    This post is awesome!! very very helpful for me! haha.

    Anyway, here is one more question.

    Can I change the shortcuts? Xournal’s shortcuts aren’t convenient.

  13. Fido Permalink →

    Thanks for this post.

    Xournal do the job : annotate !