Q: my mail is open but no window is showing? I'm receiving mail but can't open the window to see it?

Please quit Mail. Force quit if necessary.

Back up all data before proceeding.

If you're running OS X 10.11 ("El Capitan") or later, triple-click anywhere in the line below on this page to select it:

~/Library/Mail/V3/MailData

If you're running an older version of OS X, use this line:

~/Library/Mail/V2/MailData

Copy the selected text to the Clipboard by pressing the key combination command-C. In the Finder, select

          Go ▹ Go to Folder

from the menu bar. Paste into the box that opens by pressing command-V, then press return.

A folder window will open. Inside it there should be files with names as follows:

          Envelope Index

          ExternalUpdates.storedata

Move those files to the Desktop, leaving the window open. Other files in the folder may have longer names that begin as above. Move those files, if any, to the Trash.

Relaunch Mail. It should prompt you to re-import your messages. You may get a warning that the index is damaged and that Mail has to quit. Click OK. Typically, the process takes a few minutes, but it may take hours if you have gigantic mailboxes. In that case, you may be able to speed things up by temporarily adding your home folder to the Privacy list in the Spotlight preference pane. Remove it when Mail has finished importing.

If the import operation stalls or fails with an error message, quit Mail, delete the two new index files (keeping the original ones that you moved to the Desktop), and try again. According to many reports, the second attempt may succeed after the first one has failed.

Test. If Mail now works as expected, you can delete the files you moved to the Desktop. Otherwise, post your results.

This problem just cropped up on my computer also.  Followed instructions and when I re-open mail it shows importing the mail accounts but still nothing.  The dock shows mail open and I have 10 new messages but no window opens.  I tried the solution 3 times. 

MacBook Pro mid2009 OS X El Capitan 10.11.4

I did a little more research and found reference to someone who had tried to use a mail template.  I had done that earlier in the day.  In system preferences, I unchecked mail for that internet account and followed the procedure again.  This time it worked.  Thanks.

Thanks for this help.  It did lead to success only after trial and error of unchecking mail in my 3 internet accounts as referenced below by "rrmpm".  Thanks to both of you for your help.