'''If you have a POP mail account:''' Pop mail accounts can only see the Inbox on the server. This is not a TB quirk, this is how all Pop mail accounts work no matter what email client. There is a workaround. You would need to logon to your webmail account via a browser and move those messages into the Inbox. Suggest you do this one folder at a time as it is easier to move them when downloaded. then in Thunderbird click on Get Messages to download. Create a suitable folder and move the emails out of Inbox into the new folder. repeat until all emails are downloaded. '''If you have an IMAP mail account:''' You need to subscribed to see those folders. In Thunderbird right click on a remote folder and select "subscribe" to get to the dialog box that lets you specify which folders should be subscribed.