mail folders disappeared on OS X El Capitan

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Try re-indexing the mailboxes. This can take awhile if you have a lot of mail.

Reindex messages For El Capitan, try looking in V3. Sierra use V4

Reindex messages (2) See post by Linc Davis

That didn't work for me.

The correct answer is that the new Mail has a "show/hide" button for mailboxes WHICH IS INVISIBLE unless you mouse over it. In the mailboxes menu, run your cursor over the "On My Mac" and the symbol "+" will become visible, along with the "Show" option next to it. Click "show" and your mailboxes will appear.
(I don't have the slightest idea why Apple decided to make a critical menu item invisible.)

This solved my problem! I'd spent a fruitless 30min on the phone with Apple support and they basically said sorry, your "stored" folder had vanished after reinstalling OSX, and that was that.

Thank You!!

Have you found a resolution to this problem? All of my work subfolders (client folders) are missing, but everything else is showing us as usual. No idea what to do. Literally client history of projects and all communication. The "uncheck/recheck" fix didn't work. HELP!

For the love of God... every time there's an update it's the same problem!! Why can't apple fix this, it's so simple!!!!

Do this and save yourself the nightmare of dealing with support ever again!

https://soundsupport.biz/2016/10/09/how-to-reveal-missing-mail-folders/

I also have this same problem since upgrading to El Capitan on both my MacBook and my iMac. The mailboxes are still working properly on my iPhone and iPad with iOS 9.0.2 but are completely missing in Mac Mail.

Found the (an?) answer.

Go to Mail > Preferences > Accounts, and then uncheck the "Enable this account" option and then re-check it.

Worked for me 🙂

Worked the first time - Awesome...

Thank you! I was freaking out about my folders, and your suggestion worked! Easy!

Okay thanks! Inbox returned. Outbox still missing. Any thoughts how to get it back?

MrAll - The Outbox is only visible while it has mail in it, waiting to be sent. After the mail has gone (into the Sent box) the Outbox disappears.

My mistake, I had to translate it from my language. What I meant is that (old) data from my Sent box is missing (or not showing).

I have to say that, even though this fix is simple, it is anything but intuitive and not automatically importing folders is just bad design.

Mail account subfolders lost after update 😠