There is no single "best PDF annotation app," because marking up a PDF and keeping what you learned from it are two separate jobs. One job is ink on the page: highlighting, drawing, scribbling in the margin. The other is durable notes: the handful of ideas you want to find, review, and think with a month later. Most people pick a tool for the first job and quietly lose the second. So pick by need, and don't ask one app to do both well.
Pick by what you actually need
| Your need | Reach for | Bad fit for |
|---|---|---|
| Handwriting on lecture slides and PDFs with a stylus | GoodNotes or Notability | Anyone who wants searchable, restructurable text later |
| Everyday document work: fill forms, sign, edit, merge | PDF Expert or Adobe Acrobat | Deep reading where you want to extract and connect ideas |
| Research reading: excerpt, connect, and pull annotations into notes | Highlights or LiquidText | Casual markup or quick one-off form signing |
| Free, cross-platform PDF markup on any device | Xodo | People who want polished handwriting or research extraction |
| Where the ideas you pulled out go to live and get searched | Clair Mind | Annotating the PDF itself (it does not do that) |
Handwriting on the page: GoodNotes and Notability
If you hold an Apple Pencil and want to write directly on slides and PDFs, this is a short conversation. GoodNotes and Notability own handwritten markup: smooth ink, palm rejection, and highlighters that snap to text. They are the natural home for structured markup on a tablet, and they pair well with note-taking on an iPad.
They are a bad fit if your real goal is text you can search, restructure, and reuse. Ink is hard to reorganise, and handwriting search only mostly works. Many people write in class, then type the keepers into a separate system afterward, which is a sensible workflow, not a failure.
Document work: PDF Expert and Adobe Acrobat
For the office job of PDFs (filling forms, signing, editing text, merging files) PDF Expert on Apple devices and Adobe Acrobat almost everywhere are the reliable picks. Acrobat's form handling and signing are hard to beat. Both are overkill for deep reading, and both push their strongest features behind paid tiers, so check what the free tier actually includes before you commit.
Reading to learn: Highlights, LiquidText, and Xodo
This is the category most people mean when they say "annotate a PDF for study." Highlights is built to turn your highlights, images, tables, and citations into notes you can export to other apps. LiquidText lets you pull excerpts out and physically connect ideas across long documents, which suits legal, medical, and academic reading. Xodo is the free, cross-platform workhorse when you just need solid markup on any device.
The trap here is that even these extraction tools leave you with a pile of highlights, and a highlight is not yet a note. The real work is taking notes from a book or article by rewriting the idea in your own words, which is also how you actually remember what you read. Highlighting feels like learning and mostly is not.
Where the ideas live afterward: Clair Mind
Here is the honest part: Clair Mind does not annotate PDFs. It has no ink, no page markup, no highlighter. If marking up the document is the job, use one of the tools above. Full stop.
What Clair Mind is good at is the step after. Once you have squeezed a paper or a book down to the two or three ideas worth keeping, those ideas need a calm, searchable home that follows you off the tablet. Capture each one as a plain note on your phone in a couple of taps, and later you can ask across all of them in plain language instead of digging through PDFs you will never reopen. That is the difference between annotating a source and building research notes you can think with, and it is the heart of progressive summarization: the PDF holds the highlights, your notes hold the meaning.
How to actually choose
- Name the job first. Writing on the page, doing document paperwork, or reading to learn. Those are three different tools, and forcing one app to cover all three is why people end up frustrated.
- Separate the highlight from the note. Extraction tools like Highlights and LiquidText get annotations out of the PDF; a real note is you restating the idea, kept somewhere you will look again.
- Plan for the reopen. A marked-up PDF you never revisit is wasted effort. Whatever you use to mark up, make sure the ideas end up somewhere they come back to you when you need them.