Have you set up your Account Settings > Junk Settings for each mail account? Have you trained Thunderbird so it knows examples of what is Junk and what is not junk? '''Set up each mail account junk controls:''' In 'Account Settings' * Select 'Junk Settings' for the mail account. * Select 'Enable adaptive junk mail controls for this account' * Select all necessary address books to act as a whitelist. * If required - I personally do not use this - select 'Trust junk mail headers set by eg: Spamassassin' - Do not select it if not sure. * Select 'Move new junk messages to'; If you are using a '''POP''' mail account: * Select 'Junk folder on' and choose the mail account If using '''IMAP''' mail account: * Select 'Other' and choose the server subscribed folder name eg: 'Spam on account email address' '''Set up the default junk mail settings:''' * Settings > Privacy & Security * scroll to 'Junk' section * Select: 'When I mark messages as junk' * Select 'Move them to the accounts junk folder' * select 'Enable adaptive junk filter logging' '''How to train the junk filter can be found here:''' * https://support.mozilla.org/en-US/kb/thunderbird-and-junk-spam-messages#w_training-the-junk-filter Please note it is just as important to train what is junk and what is not junk. It can take a couple of weeks to really get the junk controls working well. It improves as it learns.