Extract PDF Annotations
The Extract PDF Annotations tool reads the annotation layer of a PDF and turns every highlight, comment, sticky note and markup into clean, structured text you can reuse. When you highlight a sentence in Adobe Acrobat, Apple Preview, Microsoft Edge, Foxit or almost any modern reader, the highlight is not painted onto the page as pixels, it is stored as a separate annotation object that records what was marked, in what colour, by whom, and when. This tool pulls those objects out and, for text markup like highlights and underlines, matches each one back to the words underneath it, so you get the actual quoted text rather than just a coloured rectangle.
This matters because annotations are usually the most valuable part of a document for a reader. A researcher highlighting a journal article, a lawyer marking up a contract, a student working through a textbook, or an editor leaving comments on a draft are all creating a condensed version of the document, the parts that matter. Copying those out by hand, one highlight at a time, is slow and error-prone. Exporting them as Markdown, CSV or JSON lets you drop them straight into a notes app like Obsidian or Notion, a spreadsheet, a reference manager, or a script.
Like every core ToolzPedia tool, extraction happens entirely in your browser using the open-source PDF.js engine. Your PDF is never uploaded to a server, which is essential when the document is a confidential contract, an unpublished manuscript, patient notes or any other sensitive material. You can close your connection after the page loads and the tool will still work.
Use the tool edit
PDF only · Annotations are parsed in your browser · Max 100MB
How to use Extract PDF Annotations edit
Follow these steps to use the tool:
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Upload PDF
Drop or select a PDF that contains highlights, comments or sticky notes.
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Auto-extract
The tool reads the annotation layer of every page and matches each highlight to the text underneath it.
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Review & filter
Browse annotations grouped by page, filtered by type, with author, colour and date.
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Export
Copy as Markdown, or download the whole set as Markdown, CSV or JSON for your notes app or spreadsheet.
Frequently asked questions edit
Use cases edit
Highlight the key claims and methods across a stack of papers, then export every highlight to Markdown and paste it into your literature matrix or notes vault.
Pull every marked clause and reviewer comment out of a contract into a CSV so you can track issues, owners and resolutions in a spreadsheet.
Turn a semester of highlighted PDF chapters into a single revision document grouped by page, ready for flashcards or summaries.
Collect the sticky-note comments several reviewers left on a draft into one structured list with author names and dates.
Export annotations as JSON to import them into a knowledge base, a custom script, or an AI summarisation workflow.
How it works edit
A PDF stores annotations in an /Annots array attached to each page. Each entry is a dictionary describing its subtype (Highlight, Underline, StrikeOut, Squiggly, Text for sticky notes, FreeText, Ink and so on), a rectangle or set of quadrilateral regions describing where it sits, an optional colour, an optional author (the /T field), optional contents (a typed comment), and creation and modification dates.
The tool asks PDF.js for the annotation list of every page with page.getAnnotations(), and separately for the page's text layer with page.getTextContent(). For text-markup annotations such as highlights, it takes the quadrilateral regions the highlight covers and finds every text run whose position overlaps those regions, then orders the matches top-to-bottom and left-to-right to rebuild the quoted passage. Sticky notes and free-text annotations carry their message directly in the contents field, so those are read as-is.
Because the quoted text is recovered from the text layer, it depends on the PDF actually having a text layer. A born-digital PDF produced from Word, LaTeX or a web page has one. A scanned document is a photograph of a page with no text data, so for those the tool can still list the highlight regions and any typed comments, but not the underlying words unless the file has been run through OCR first.
Tips and best practices edit
- If a highlight comes back with a few extra words at the start or end of a line, it is because the highlight region slightly overlapped neighbouring text. Trim it in the exported text, it does not affect the original PDF.
- Use the type filter to export only highlights, or only comments, when you need a focused list.
- Export to CSV when you want to sort, tag or assign annotations in a spreadsheet; export to Markdown when the destination is a notes app; export to JSON when a script or another tool will consume it.
- Author names only appear if the person who made the annotation set an identity in their PDF reader. Many readers leave this blank by default.
- If your highlights do not appear at all, they may have been "flattened" into the page when the file was printed to PDF or exported. Flattened highlights are pixels, not annotations, and cannot be recovered as data.
Common mistakes edit
A scanned PDF has no text layer, so highlighted words cannot be recovered. Run the pages through an OCR tool first to add a text layer, then extract.
Some workflows merge annotations permanently into the page image. Once flattened, a highlight is indistinguishable from the rest of the page and holds no extractable data. Keep an un-flattened copy if you plan to extract.
The small popup windows that display a comment are separate annotation objects. The tool reads the comment from the parent markup, not the popup, and skips empty popups to avoid duplicates.
There is no need to send a confidential PDF to an online extractor. This tool runs in your browser, so the file never leaves your device, use that to your advantage with sensitive documents.
Comparison edit
How browser-based annotation extraction compares to common alternatives:
| Aspect | ToolzPedia (browser) | Copy-paste by hand | Desktop PDF suite (paid) |
|---|---|---|---|
| Privacy | File stays on your device | Stays local but tedious | Local, but often cloud-synced |
| Speed | Whole document at once | One highlight at a time | Fast, once configured |
| Quoted text recovery | Automatic from text layer | Manual selection | Usually yes |
| Export formats | Markdown, CSV, JSON | Whatever you paste into | Varies, often proprietary |
| Cost | Free, no account | Free but slow | Subscription or licence |
Related tools edit
Other free pdf tools available on ToolzPedia:
Merge PDF
Combine multiple PDF files into one. Drag to reorder pages before merging.
Split PDF
Extract specific pages or split a PDF into multiple files by page range.
Compress PDF
Reduce PDF file size without sacrificing quality. Perfect for email.
JPG to PDF
Convert JPG, PNG or any image to a professional PDF document instantly.
Sign PDF
Add your digital signature to any PDF document directly in the browser.
Protect PDF
Add password protection and encryption to sensitive PDF documents.
See also edit
- All pdf tools on ToolzPedia
- All tools, every utility in the encyclopedia
- Tutorials and guides related to pdf tools
- Report a bug or request a feature