How to Delete Kindle Highlights (Device, App, Amazon, File)

A Kindle highlight lives in more than one place, so deleting it means knowing which copy you are looking at. Here is how to remove a highlight on the Kindle, in the app, at Amazon and from My Clippings.txt, why some come back, and how to keep the ones you meant.

Deleting a highlight, wherever you are

On the Kindle
Tap the highlighted text and choose Delete from the toolbar. For a list view, tap the top of the page, open the notebook (Notes or Notebook, depending on the software) and use each entry's menu. Deletions sync to your other devices when they next connect.
In the Kindle app
On iPhone, iPad and Android, tap the passage and choose Delete, or delete from the book's notebook. On Kindle for PC and Mac, click the highlight, or open Show Notebook. Kindle for Web at read.amazon.com offers Delete on each highlight too.
At Amazon, read.amazon.com/notebook
Your Kindle notebook page lists every highlight from books bought from that Amazon store. Each has a menu with Delete. This is the master copy your devices sync from, so a deletion here sticks. There is no select-all: one highlight at a time.
In My Clippings.txt
The Kindle appends every highlight, note and bookmark to documents/My Clippings.txt and never removes a line, even when you delete the highlight in the book. Over USB you can edit the file or delete it outright; the Kindle starts a fresh one. Everything from personal documents is only here, so copy it out first.
Popular Highlights are not yours
The dotted underlines showing what other readers marked are switched off under Settings, Reading Options, Popular Highlights. Nothing of your own is deleted by turning them off.
When a deleted highlight comes back
A device that was offline when you deleted can sync the old copy back. Delete again while online, or delete at read.amazon.com/notebook. Highlights in personal documents never sync through Amazon at all; they exist only on the device that made them.

Tidy up without losing the good ones

Most people who want to delete highlights are really trying to end up with a clean set of the ones worth keeping. That is easier outside the Kindle.

Clippings.io imports every highlight from all the places Amazon keeps them, with the browser extension for Amazon-bought books and My Clippings.txt for everything else, and removes the duplicates. Then you delete, edit and tag in one place: a single highlight, a whole book, or an entire import. Deleted highlights sit in Deleted Items until you empty it, and Clippings.io remembers what you removed so the next import does not bring it back.

What Clippings.io does not do is change anything on Amazon or on your Kindle. It only reads from them. So you can clear My Clippings.txt for a fresh start, or leave the mistakes on the device, and still have exactly the set you want to export to Notion, Evernote, Word, PDF, Markdown or anywhere else on the export destinations list.

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Deleting Kindle highlights: questions

How do I delete a highlight on my Kindle?
Open the book, tap the highlighted text, and choose Delete (the bin icon) from the toolbar that appears. Or tap the top of the page, open the notebook (Notes or Notebook, depending on the software), find the highlight and choose Delete from its menu. The change syncs to your other devices the next time they connect.
How do I delete highlights in the Kindle app?
On iPhone, iPad or Android, tap the highlighted passage and choose Delete, or open the book's notebook, tap the highlight and delete it there. On Kindle for PC and Mac, click the highlight and choose Delete, or use Show Notebook. The Kindle for Web reader at read.amazon.com also offers Delete on each highlight.
Can I delete all my Kindle highlights at once?
Amazon has no bulk delete. At read.amazon.com/notebook you delete highlights one at a time from each highlight's menu, and there is no select-all on the device or in the app. The one thing you can clear in one go is My Clippings.txt on the Kindle itself, by deleting the file over USB, but that removes every highlight and note from every book and personal document at once, and it does not touch the copies Amazon holds.
Why do deleted highlights come back?
Usually because a device or app was offline when you deleted, and another device synced the old copy back. Delete the highlight again while the device is online, or delete it at read.amazon.com/notebook, which is the copy the others sync from. Highlights in personal documents and sideloaded books never sync through Amazon, so those only exist on the device where you made them.
How do I delete clippings on a Kindle?
Clippings are the entries in My Clippings.txt, the file where the Kindle appends every highlight, note and bookmark. Deleting a highlight in a book does not remove its line from that file. To clear it, connect the Kindle to a computer with the USB cable, open the documents folder, and delete or edit My Clippings.txt; the Kindle starts a fresh file with your next highlight. Copy it somewhere first, or import it into Clippings.io, if there is anything in it you want to keep.
How do I turn off Popular Highlights?
Those dotted underlines are other readers' highlights, not yours. On the Kindle, open Settings, then Reading Options, and switch Popular Highlights off. The Kindle app has the same switch in its reading settings. Turning them off does not delete anything of your own.
If I delete a highlight in Clippings.io, is it deleted on my Kindle?
No, and the other way round is also no. Clippings.io only reads from Amazon and from My Clippings.txt; it never writes to them. Deleting in Clippings.io moves the highlight to Deleted Items, where you can restore it or delete it for good, and Clippings.io remembers the deletion so the same highlight is not imported again next time. Deleting on the Kindle removes it from Amazon's copy but leaves whatever you already imported into Clippings.io untouched.

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