Skip to Main Content

Zotero at University of Waterloo: Zotero 6.0

This guide will help you use the free online citation and research management tool Zotero to organize citations from Library catalogs and databases.

Beta release

Zotero released version 6.0, which includes many new features.

  • Open PDFs in a new built-in reader within the main Zotero window, in a new tabbed interface
  • Clean up metadata for items while viewing their PDFs
  • Mark up PDFs with highlights, notes, and image annotations
  • Add annotations to Zotero notes with automatic citations, in a powerful new note editor
  • Cite other items directly in notes using Zotero’s familiar citation dialog
  • Insert notes into your Word, LibreOffice, and Google Docs documents with active Zotero citations for automatically generating bibliographies
  • Export notes to external Markdown editors with links back to Zotero items and PDFs

Zotero PDF Reader and Note Editor

In preferences, you have the ability to open PDFs using the program you've designated as your System Default, or browse for another program on your computer. In Zotero 6.0 you can choose to open them with Zotero.

option to open PDFs using Zotero

The PDF opens up in a tabbed interface. 

pdf open in zotero program

In the menu that appears in the upper right-hand corner, the first option opens up the item details pane. As many articles include bibliographic information on the first page, this will assist you in verifying the metadata that was imported by Zotero. 

The second option opens up a notes panel. Click on the + and choose to add a new note, which will open up the note editing window. The other option is to Add Item Note from Annotations.

item notes option


highlighted text and a comment

In Zotero's PDF viewer, you can highlight text and add comments, and add tags to your comments. If you then choose the option Add Item Note from Annotations, the highlighted text and comments are extracted and put into the notes pane. 

annotations that were extracted from PDF

The annotations are automatically saved. Like all Zotero library data, the annotations you create will automatically sync across all your Zotero installations. You can also create PDF annotations in group libraries.

The annotations in the notes include live links that will return you to the place in the PDF where you made the annotation.

It will always remain possible to set Zotero to open PDFs in an external reader if you prefer one to the internal reader. Externally created highlights and notes show up in the PDF reader and can be added to Zotero notes as easily as annotations you create in Zotero.

Adding notes to word processors

After updating to Zotero 6.0 you may need to reinstall the Zotero word processor plugin. An "Add Note" button has been included in the menu.

zotero menu with add note option

When you use the Add Note feature, you can choose from a list of notes which you want to add to the document. The annotations in that note will be inserted, along with citations to to the annotated document.

word document showing inserted annotations and corresponding citations

Syncing with the Zotero IOS app

The PDF reader syncs seamlessly with the Zotero iOS app, allowing you to highlight and take notes on your iPad or iPhone and then quickly pull those annotations into a note or word processor document when you're back at your computer. PDFs will open automatically to your current page, no matter what device you last used.

Embedded images in notes

In addition to natively supporting annotations and citations, Zotero notes now fully support embedded images. You can drag in images from your computer or the web, and they’ll sync to your other devices. You can also create an “image annotation” in the PDF reader and drag it straight into a note to easily create a cited image in your document.