It sounds like your mail files were corrupted. Rebuilding the index file just cleared the view of the messages, they were already gone prior to the repair action. You'd need to restore them from a recent backup of your Thunderbird profile folder, which you hopefully did create before. http://kb.mozillazine.org/Thunderbird_:_FAQs_:_Backing_Up_and_Restoring Corruption is often caused by anti-virus software messing with Thunderbird mail files. It is therefore recommended to create an exception for the Thunderbird profile folder, so that the real-time scanner won't attempt to scan the profile with your mail. For more information on the profile location see http://kb.mozillazine.org/Profile_folder_-_Thunderbird Also see http://kb.mozillazine.org/Keep_it_working_-_Thunderbird