"AI PDF annotation" gets searched by two groups of people who want opposite things. One wants AI help marking up a PDF — highlighting, commenting, and saving those annotations to the file. The other wants AI to help them understand a PDF — explaining dense passages and pointing to the parts that matter. Most roundups blur the two. This guide separates them, so you pick a tool that does the thing you actually need.
Two very different meanings of "annotate"
- AI-assisted markup — tools that let you (or an AI) highlight, comment on, and mark up a PDF, then save those annotations back into the document to share or keep. This is the classic PDF-annotation workflow, now with AI features layered on.
- AI reading layers — tools that highlight and explain passages as you read to help you understand the document, without necessarily saving markup into the file. The "annotation" here is about comprehension, not producing a marked-up copy.
Neither is better in the abstract. If your goal is a shareable, annotated PDF, you want the first. If your goal is to get through a hard document and trust what you took from it, you want the second.
AI-assisted markup tools
If you need saved highlights and comments in the file itself — for review workflows, sign-off, or collaboration — look at dedicated PDF editors with AI features. Adobe Acrobat, Foxit, and similar editors let you mark up PDFs and increasingly bundle AI summarisation and Q&A alongside the markup tools. They're the right pick when the output is an annotated document.
The trade-off is that they're editing suites first — often subscription-based, PDF-centric, and heavier than you need if you only want to read and understand. (On Acrobat's AI specifically, see our Adobe Acrobat AI Assistant review.)
AI reading layers — highlight, explain, and verify
If your real goal is understanding, a reading layer is the better fit. Sidenote sits in this camp. It's a browser reading assistant, not a markup editor — and it's worth being precise about what that means: it doesn't save highlights and comments back into your PDF. What it does is help you read and trust the document.
- Highlight to explain. Select any passage and get a plain-language explanation grounded in that passage and its surrounding context, with depth levels for how simply you want it put.
- Every answer is cited. Ask a question and each claim carries a scroll-to-source citation: click it and the PDF scrolls to the exact sentence and highlights it in place.
- Nothing invented. Claims that can't be matched to a real passage are dropped server-side, so the explanations and answers you get are anchored to what the document actually says.
- Works beyond PDFs. The same highlight-and-explain reading layer works on scanned PDFs (via OCR), web pages, Confluence, Notion, Google Docs and more.
So Sidenote's "annotation" is the reading kind: it highlights sources and explains passages to help you understand, rather than producing a marked-up file to send on.
Which type of tool do you need?
| You want to… | Reach for | Example |
|---|---|---|
| Save highlights/comments into the file | An AI-enabled PDF editor | Acrobat, Foxit |
| Understand a dense passage as you read | An AI reading layer | Sidenote (Explain) |
| Get cited answers you can verify | A citation-first reader | Sidenote (Citations) |
| Mark up and share for review | A PDF editor with collaboration | Acrobat, Foxit |