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Annotate PDFs and extract notes
What you’ll do
By the end you’ll have highlighted a PDF, extracted all annotations into a single note, and used that note’s citations in a document.
Why it matters
Reading without capture is re-reading. The built-in reader stores annotations in Zotero — linked to the exact page — so your highlights become quotable, citable material instead of a yellow blur in some other app’s folder.
Highlight on the page (1); the Notes pane collects annotations (2). Illustration, not an actual screenshot.</figcaption> </figure>
Steps
- Open the PDF: double-click the item in your library — it opens in Zotero’s built-in reader.
- Highlight: select text and click a color in the popup (or click the highlighter tool first to “lock” the color for repeated highlights).
- Add a thought: click an annotation and type in its comment field — later you’ll be glad the argument you had is attached to the quote.
- Open the Notes pane: click Notes (top right of the reader), then the + and choose Add Item Note from Annotations. Zotero creates one note containing every highlight and comment, each with a link back to the page.
- Write from the note: open the note in the left pane, copy a quotation — or click the annotation’s citation in the note and drag it into a document with the plugin’s Quick Copy. Annotations can also be dragged individually from the reader’s sidebar into any note.
- Know the one big rule: annotations live in the Zotero database, not inside the PDF file. To share a PDF with annotations visible in other readers, use Export a PDF (right-click the item) or export with annotations embedded.
Check it worked
Your item has a note (visible in the right pane’s Notes tab) listing every highlight with page links — and clicking one jumps to the exact spot in the PDF.
If it didn’t work
- Highlighting acts oddly on a scanned PDF — image-based scans can’t be text-selected; run OCR first (outside Zotero) or take notes manually.
- Your colleague’s annotations in a shared PDF confuse you — that’s the group workflow; see Group libraries.
- Reader misbehaves (cursor jumps while typing annotation notes, highlights inconsistent) → these are known product bugs in the support data, not your setup: check the Zotero forums before re-installing anything.
Last verified against Zotero 10.0.6 documentation on 2026-10-25. Zotero's interface changes between versions — if a step does not match what you see, check the official documentation linked above and report the lesson via the “Report an outdated lesson” issue template.