Top 3 Free Tools to Extract Annotations from PDFs

If you highlight, comment, or annotate PDF files often, you’ll want a tool that can extract those annotations automatically. Whether you're doing research, reviewing a paper, or working with reports, here are the top 3 free tools to help you extract highlights, comments, and notes from PDFs.

1. PDF Highlight Extractor (Free Web Tool)

PDF Highlight Extractor is a browser-based tool that lets you:

• Upload any PDF
• Extract highlights, comments, and pop-up notes
• Export them as a CSV file (Word and Excel support coming soon)

Try PDF Highlight Extractor →

2. Adobe Acrobat Reader (Free Desktop Tool)

Adobe Acrobat Reader allows you to annotate PDFs with highlights and comments. While it doesn’t have a built-in “export all annotations” button, you can:

• View all annotations via the Comments pane
• Manually copy and paste them
• Use third-party scripts or plugins to automate export (e.g., PDF-XChange, JavaScript plugins)

3. Zotero + Zotfile (For Researchers)

Zotero is a reference manager used by academics. With the Zotfile plugin, you can:

• Extract annotations from PDFs added to your Zotero library
• Automatically store highlights and notes as separate Zotero notes
• Keep everything organized with citation metadata

Which Tool Should You Use?

- Use PDF Highlight Extractor for quick, no-login exports.
- Choose Adobe Acrobat if you already use Adobe tools daily.
- Go with Zotero + Zotfile if you're managing academic PDFs and citations.