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How To Annotate PDFs While Reading Them On Kindle?

Annotations disappear after reading PDFs on Kindle Paperwhite, making highlighting and note-taking a headache for my research papers.
2025-07-10 02:54:49
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11 Answers

Best Answer
Daniel De La Haza
Daniel De La Haza
The Kindle's annotation of PDFs is rudimentary and not nearly as useful as that for EPUBs. Annotating PDFs on the Kindle is best done by first converting the PDF to a Kindle-friendly format using software like Calibre, or by using the ‘Send to Kindle’ functionality and hoping for the best. I recently read ‘Accidentally Marked By The Alpha King’ – a werewolf romance – which was a fun read for the Kindle, no fuss needed. The whole plot centers on a mistaken, permanent supernatural marking of the protagonist by the titular Alpha King.
2026-08-05
Grayson
Grayson
I have been using my Kindle for years, and, for me, annotating PDFs is one of the best ways to read through a text. When I open a PDF on my Kindle, I can select a chunk of text and then highlight it by pressing and holding on the text and then dragging the handles of the selected text to change the size of the selection. A small toolbar then drops down from the top of the screen that includes underlining as well as the ability to add notes to the highlighted section of text. Typically, I will read through a section of text and jot down a number of thoughts quickly, at times linking to another book that the section reminded me of, at times the section giving me an idea that I need to explore in more detail. The annotations are then synced to my Kindle reading apps on my phone and tablet, allowing me to reference my notes on the text at a later date. When I need to engage in more in-depth note taking on a section of text, I use the ‘Add Note’ option that allows for margin type note taking. While annotating PDFs on my Kindle is not as easy as it is with EPUBs, it gets the job done. I also use Kindle’s ‘My Clippings’ feature to organize the annotations that I have made to a particular book, exporting them as a text file.
2025-07-12
Owen
Owen
I read a mix of fiction and non-fiction on Kindle, mostly in PDF form, and I’ve found annotating these documents to be incredibly useful. After opening up a PDF in Kindle, you can highlight by pressing and holding on a word and then selecting underline, highlight, note, or bookmark from the options that appear.

For heavy annotators like myself, there is also the option to export the ‘My Clippings’ file for the PDF and organize it in a spreadsheet or even note-taking app like Notion. The Kindle annotations lack the robust tools of a PDF annotation software but suffice for my casual reading and annotation needs. Color coding and even drawing tools would be wonderful but in the mean time simple margin notes are sufficient.

Pinch to zoom in on text before highlighting to ensure it is readable. Note that as with reading, Kindle can make poorly formatted PDFs worse, but zooming out usually suffices to fix. People who annotate a lot of PDFs might also look at LiquidText, an annotation app on iOS and Android that integrates with the Kindle, but is not as seamless as the Kindle's native highlighting.
2025-07-16
Ruby
Ruby
Kindle annotating PDFs is like having a conversation with the text. I use highlights to point out important passages and use notes to have a conversation with the text, to react to it, to connect with other works etc. The toolbar is very minimalistic but it has everything you need: highlights, underlines, notes. Bookmarks are usually used to mark the places where the PDF needed to be bookmarked in order to read it later.

Synching annotations across my Kindle devices is also really seamless – I can be in the middle of reading a book on my Kindle Paperwhite, abandon it mid-sentence on the bus and pick up where I left off on my phone in the afternoon. I can then export my ‘My Clippings’ file as a PDF and then import that into a tool like Obsidian where I’d link those annotations to other relevant notes within other projects.

Occasionally, when I am reviewing image-rich PDFs or particularly complex documents, I end up switching to a tablet and using a stylus instead, but this is more the exception than the rule, and typically I find that Kindle is quite sufficient for any kind-of casual markup of typical text-based PDFs.
2025-07-16
Eric Zenón
Eric Zenón
Accidental highlights are the worst – they can happen by accident when you brush against a page with your hand or sleeve. I periodically go back through my highlighted sections to remove any stray highlights. To avoid highlights altogether while reading, you can temporarily disable the touchscreen by going to the top of the page and selecting ‘Lock Screen’ (looks like a padlock). This is also useful if you’re leaving your Kindle with someone else to read, or if you’re reading in a crowded location and don’t want anyone to accidentally highlight or annotate your book. Just remember to ‘unlock screen’ again when you want to start highlighting or annotating.
2026-07-31

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