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Research Guides

Highlighting and Commenting on PDFs Using Adobe Acrobat

Although you cannot edit PDFs in Zotero directly, Zotero will save the annotations you make from PDFs in other programs, such as Adobe Acrobat.

  • Double clicking the PDF in Zotero will open it up in your default PDF editor.
  • To change Zotero's default PDF editor, in the top left of the window click "Edit > Preferences". Under General, change "Open PDFs using System Default" to your preferred program.
  • After opening your PDF, you can annotate and highlight relevant portions
  • When saving your PDF, you can save it to the Desktop, delete the old PDF from Zotero, and attach the new one. Or, you can overwrite the file directly in Zotero's storage.

Importing Annotations Using Zotfile

Zotfile is an open source plugin for Zotero that can automatically extract annotations and save them in a Zotero note. You can use this to keep track of quotes you wish to cite, or important ideas to remember without opening the PDF directly. Zotfile can also be used to automatically batch rename and move attachments, and sync PDF's with a tablet.

  1. Download the Zotfile plugin from
  2. Install Zotfile in Zotero
    • Open Zotero and choose Tools > Addons from the menu in the top left
    • In the new window that appears, click the gear in the top right and choose "Install Add-On From File..." and select the file you downloaded from Zotfile
    • Restart Zotero
  3. Right click your annotated PDF in Zotero or it's parent element and choose "Manage Attachments > Extract Annotations". A new note will appear that contains all your PDF annotations with the date and links to that page in the text.

If you want to edit Zotfile preferences, they can be found under "Tools > Zotfile Preferences..."

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