Just noticed you said you had restarted Firefox.
There is another possibility -- corrupt localstore.rdf

• 'Corrupt localstore.rdf' - MozillaZine Knowledge Base
  http://kb.mozillazine.org/Corrupt_localstore.rdf

I think that is what others see as well, until they restart Firefox. I always use the Bookmarks sidebar ("Ctrl+B"), or the Bookmarks Manager ("Ctrl+Shift+B") to work with bookmarks, and the bookmarks toolbar itself which mostly shows folders.

For help working with your bookmarks and history see

• Bookmarks - MozillaZine Knowledge Base -- http://kb.mozillazine.org/Bookmarks
• Sorting and rearranging bookmarks - Firefox - MozillaZine Knowledge Base -- http://kb.mozillazine.org/Sorting_and_rearranging_bookmarks_-_Firefox
• Viewing the browsing history - Firefox - MozillaZine Knowledge Base -- http://kb.mozillazine.org/Viewing_the_browsing_history_-_Firefox

A possible cause is a problem with the file places.sqlite that stores the bookmarks and the history.

• http://kb.mozillazine.org/Bookmarks_history_and_toolbar_buttons_not_working_-_Firefox

Thanks for your replies!

cor-el, It's not my bookmarks that are missing, it's just that a huge part of them doesn't appear in the menu any more.

dmcritchie, thanks especially for rethinking and coming back here. Your link brought a very promising headline ("Bookmarks appear in the Bookmarks Manager but not in the main menu and can't be edited"), but the link was kind of misconnected and lead to some 6 year old topic where the term menu didn't appear.

Nevertheless, I tried replacing the localstor.rdf file in two ways (backup and by FF itself) but nothing changed so far.

Did you look in the Bookmarks Sidebar?
View > Sidebar > Bookmarks

The Unsorted Bookmarks folder doesn't appear in the Bookmarks Menu bar drop-down, but it does appear in the Library and the Sidebar.

the-edmeister, thanks, my unsorted bookmarks appear in the menu like they did before. I'm having problem with the folder "Bookmarks Menu" (hope this is the correct translation).

BTW: Old FF2 does display the bookmarks menu, whereas 3.6 doesn't.

You can still try a test for a corrupted file places.sqlite because that seems to happen a lot on Mac. Mac uses internal SQLite. On all other platforms SQLite is part of the Firefox installation.

Do you mean the menu bar as maintained by the Mac OS at the top of the screen?

Did you try to reset the Firefox plist file or repaired the permissions?

Go to "Library > Preferences" and remove the plist file for Firefox (org.mozilla.firefox.plist).

• http://guides.macrumors.com/Deleting_Preferences_Files
• http://guides.macrumors.com/Repairing_Permissions

Tadaa: places.sqlite was the culprit!

Thanks, cor-el, for being insistent! :)

You're welcome.