How I would go about this depends on how many messages, and how many folders are affected. '''View|Folders|Unread''' will list all the folders containing unread messages. You can then select each folder and hit shift+c on each one to mark all its contents as read. There is also an option to do this via a right-click ("Mark folder read") if you prefer to mouse everything. I have become fond of Saved Search folders for managing email. For instance, I have one named Unread which simply collates all unread (actually, "new") messages into a single virtual folder. You set this up using a dialogue very much like that used for filters, so you can add rules about age, so as to exclude recent (today's?) unread messages. (And then I usually make my Saved Search folders into tabs, using the Quickfolders add-on, but that's another story.) As to why this has happened… Do you use CCleaner? This might have erased a file that stores the "read/unread" status. Your server may have had a hiccup. Thunderbird may have had a hiccup and failed to save a file that remembers read/unread status. Your computer may have had a hiccup and failed to update a file. Unless this continues happening, and predictably, it's unlikely that we'd ever be able to work out exactly what happened.