Turn a marked-up PDF into clean notes. The tool reads every highlight, underline, strikeout and comment, recovers the text under each highlight, and lets you export it all with page numbers and colors.
Last updated:
Types
Colors
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How to use the Extract Highlights from PDF
Open your annotated PDF by dropping it into the box or clicking to choose it.
Wait a moment while every page is read and the text under each highlight is recovered.
Filter the list by type, color or keyword, and choose whether to sort by page or by color.
Press Copy Markdown to paste your notes elsewhere, or download them as Markdown, TXT or CSV.
How the highlighted text is recovered
A PDF highlight does not store the words you marked. It stores QuadPoints: four corner points for each highlighted line, plus a color, an optional comment (Contents), an author (T) and a modification date (M). To get the words back, the tool reads the text layer of the page and keeps the characters whose position falls inside those quadrilaterals, line by line. Words broken with a hyphen at the end of a line are joined again.
Annotation
PDF subtype
What you get
Highlight
Highlight
Marked text, color, attached comment
Underline
Underline
Underlined text and comment
Strikeout
StrikeOut
Struck-through text (useful for proofreading)
Squiggly
Squiggly
Text marked with a wavy line
Sticky note
Text
The note text, author and date
Text box
FreeText
The typed text
Reply
Any, with IRT
Shown under the comment it answers
Tips for better notes
Use colors with meaning. For example yellow for key ideas, green for definitions and pink for questions. Sort by color here to get each group together.
Scanned books need OCR first. A scan is just a picture of text, so there are no words under the highlights. Run OCR to add a text layer, then highlight.
Paste into your note app. The Markdown export puts each page under a heading, quotes under > and comments as bullet points, ready for Obsidian, Notion or a Markdown editor.
Clean up afterwards. Once your notes are saved, you can share a clean copy of the PDF with Remove Annotations from PDF.
Frequently asked questions
How do I export highlights from a PDF?
Drop the PDF into the box above. Every highlight, underline, strikeout and comment is listed with its page number and color. Press Copy Markdown or one of the Download buttons to save your notes.
Why is the highlighted text missing or slightly off?
Highlights store only the position of the colored area, so the text is recovered by matching that area with the words on the page. Scanned pages without a text layer have no words to match, and some PDFs place characters in unusual ways, which can add or drop a letter at the edge of a highlight.
Which PDF readers' highlights are supported?
Any app that saves standard PDF annotations, including Adobe Acrobat and Reader, macOS Preview, Microsoft Edge, Foxit, Okular, Xodo, PDF Expert, GoodNotes exports and Zotero when annotations are saved into the file.
Does it extract comments and sticky notes too?
Yes. Notes attached to highlights appear under the quoted text, and stand-alone sticky notes and text boxes are listed as Note items. Replies are shown under the comment they answer.
Can I export highlights to Notion or Obsidian?
Yes. The Markdown export uses headings per page, block quotes for highlighted text and bullet points for comments, which paste cleanly into Notion, Obsidian, Logseq and most Markdown editors.
What if my highlights were made in an app that does not save them in the PDF?
Some readers, such as certain ebook apps, keep highlights in their own database instead of in the file. Export or save the annotated PDF from that app first, then open it here.
Is my PDF uploaded?
No. The PDF is processed by JavaScript in your browser and never leaves your device.
Are all the tools on FreeToolCabin tested for quality and accuracy?
Yes! Every tool on our site undergoes automated Q/A testing in real browser environments to ensure high precision, correct output, and zero errors. If you happen to spot a bug or have a suggestion, please contact us at [email protected] and our team will review it right away.