PDF Annotaton Solution

I have been a big fan of Zotero. I was using both Endnote and Bibtex before (still use bibtex, but I export from Zotero).

I have benefited tremendously from so many comments in these forums, that I thought I would share a solution that has made managing my work much easier: annotating PDF files opened from Zotero in the web browser.

This is done by using a free PDF reader/editor called PDF-Xchange viewer. Not only does this free viewer have the ability to open pdfs from within firefox, you can also highlight and annotate the pdfs.
I have used other pdf software (such as bluebeam), but I always had to open them in a separate window. With this program installed you can just double click on a pdf in your library and it will open in the browser. You can then highlight, annotate, underline, etc. Then you can simply click 'save' and the file is saved within the zotero library. You don't have to change any file names.

I'm not sure if anyone has commented on this program before, but the fact that you can open it from within firefox has made it a dream come true. Also, the program is quite lightweight and it is free.

You can download it from

I sound like i'm plugging this, but its a solution that so many zotero users have asked for that I thought I should share. Enjoy.
  • Yes, it has been mentioned:

    Other alternatives are listed:
  • Q: How do I get FF3 to open .pdf's with PDF-Xchange viewer in the FF browser?

    I've done the following already:
    1) I've changed my system to open .pdf's with PDF-Xchange Viewer rather than Acrobat Reader
    2) In FF3 I select "Tools" > "Options" and change "PDF File" to be opened by PDF X-Change Viewer (Default). NOTE: There's no option for "PDF X-Change Viewer (in Firefox)" as there is for Acrobat reader.
    3) In PDF-Xchange Viewer I select "Edit" > "Preferences" > "File Associations" > and select the "Display PDF in Browser" option.

    Now, in FF when I select "File" > "Open File" > and choose one of the .pdf's on my hard drive, it's opened in PDF X-Change Viewer but NOT within the FF browser. I've looked for some sort of PDF X-Change Viewer plugin for the FF browser but couldn't find any.

    Q: What am I doing wrong here? Is this a bug?
  • i disabled the adobe acrobat plugin (not extension, but plugin) in firefox (I didn't uninstall it, just disabled it) and that seemed to take care of that issue. I also had that problem when I installed it.
  • one more thing. in the options i did have an option to open PDF X-Change Viewer (in Firefox) but it was not under the pdf file it was associated with "Adobe Acrobat 7.0 Document" for some reason. If you have the adobe acrobat plugin installed, then you should have this option as well.
  • Thanks for the reply ghisht. I followed your advice and disabled the Acobe Acrobat plugin for FF. However, I still was not able to see the "in Firefox" option for viewing .pdfs in PDF Xchange Viewer in the FF browser. It turns out someone was having a similar problem over on the PDF Xchange Viewer forums here:


    The problem was that the FF plugin for PDF Xchange Viewer (npPDFXCviewNPPlugin.dll) installed in the PDF Xchange Viewer file folders instead of the FF plugin folder. Once I made a copy of the .dll and moved it to the FF plugin folder I could see the option to "view in Firefox". Once I selected that option everything worked as desired.

    Hopefully this post will save someone a chunk of time in the future :)

    For the record, I have the following system:
    Vista 32bit
    Mozilla Firefox 3.0.1
    PDF Xchange Viewer 2.0
  • One last question ghisht:

    Once you have everything working are you able to use Zotero's annotation tools on the .pdf snapshot or not?

    I'm able to annotate my .pdf's using PDF Xchange Viewer's tools but somehow Zotero's annotation tools are completely overridden even though they appear in a bar in the FF browser.

    Q: Is there some way for me to tell FF to use Zotero's annotation tools instead of PDF Xchange Viewer's?
  • No--Zotero's annotation tools do not presently work with ANY third-party PDF viewer. They will only work with formats that Firefox does not need a plugin to view.
  • Yeah. You can't use zotero's annotation tools. But I enjoy those available in Xchange viewer. The cut and paste properties in the viewer allow me to copy text into zotero notes, which i do quite often.

    I have the same software configurations but did not have to copy a .dll to make it work. Go figure. Glad you figured it out. As I work with so many articles that are .pdfs, this solution has made zotero not only a complete bibliographic software, it has saved me time trying to figure out how/where to store articles.

    I'm very grateful for this powerful tool.
  • Hi Ghisht,

    Thanks for the helpful post. Before I install and use Zotero, I would make sure I can annotate pdf files in Zotero. I followed your post to install PDF Xchange Viewer as a Pro installation with Firfox pluggin. the version I downloaded is following your link
    PDF-XChange Viewer v.2.0039 2 Sep, 2008 15.30Mb Windows 2000 & Later

    however, after this install (as a pro), I can not annotate pdf files, either in the viewer software or firefox browser. A lot of functions in this version is gray and not operational, especially the comment and make up tools.

    I am wondering if this is the version you are downloading for free? I've tried couple other free versions but no luck. I also tried to install tools the PDF-Tools 4 v.4.0152 9 Oct, 2008 9.98Mb Windows 95 & Later, still annotation function does not work.

    How can I get around this and get the annotation function (for free)? Thanks
  • edited November 24, 2008
    http://www.docu-track.com/home/prod_user/PDF-XChange_Tools/pdfx_viewer/. I downloaded the PDF-XChange Viewer recommended above and would like to know how to load it inside of Firefox Mozilla? Someone upline said it would open up in Mozilla. Thanks.
  • Dear ghisht,

    You posted a comment about PDF-Xchange viewer and how it can open up in Mozilla and be used with Zotero. How is it that you were able to get PDF-Xchange viewer to load into Mozilla? Thanks.
  • 1. close Firefox (not sure if this is necessary)
    2. run the PDF-Xchange setup program
    3. During the install, Make sure that on the 'Install Components' page the "Mozilla Add-In" is selected along with whatever other components you want (non-English languages, IE plugin, etc)
    4. Select 'use as default PDF viewer' and 'Open in Browser' as options during the install.
    5. enjoy.

    Note that like any other PDF tool, PDF-Xchange is not 'used with Zotero' in any narrow sense. Because all PDF viewers are applications external to Firefox, Zotero doesn't know about your annotations, for example, so you can't search them. Still you can bring up the PDFs in your Zotero database with a simple double click, annotate to your heart's content, and re-save the file. (And it seems to work pretty well). Perhaps someday if it were possible to re-index a single file, Zotero could also include your annotations in its fulltext searches, but for now this isn't possible. (Reindexing the whole database is possible, but I don't know if this includes annotations).
  • Thanks, Scot. I'll give it a try.
  • What you can do to overcome this problem is save your pdf file as text: File > Save as Text. You can add annotations in Zotero to txt-files, so this solves the problem. It is not take too much time to save it as a txt-file.
  • edited November 5, 2009
    Pdf Exchange surprises me. I note of this viewer some time back, but ignore for the popular alternative, which I like. I then forget about it all together.

    Recently, I feel I must highlight a Pdf doc. Since I couldn't, I upload the document to Gmail as a first step. Next, I click view. In the Google preview, I then click, plain Html. After that I captured it with Zotero. It works.

    But the process mentioned above will soon wear you out, especially with large files. Preferring to get the job done faster, you start searching for add-on or websites to quickly convert the pdf to html.

    Very few are out there, in my count. Even these for a prize. A costly price, for that matter, that you will ask why you ever want to convert to html in the first place. Virus and Malware are not included in the cost.

    For me, it stops me from opening pdf within Firefox. So I filter websites for the phrase, "pdf can't open in Firefox." Off course its several variations. Trying to get my pdf open once again in Firefox overrides all my aims. In the process, I stumble on this page, I read over a year ago.

    It reminds me of Pdf Exchange. So I install it, see if it will help me to view pdf in Firefox once again. No, it didn't. But it reminds me that I can highlight with it and annotate.

    I uninstall the two other pdf viewer in my pc. Before I did this, I specify that I want Pdf Exhange to open in Firefox 3.5.5, from tool > option > applications.

    What happens after that is the surprise I talk about when I start. It opens in Firefox. And I spend an hour trying out some of the cool tools that came with it free.
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