If you are using an Imap mail account, please note that emails can get marked as junk and put in the 'Spam' folder by either the server marking email as junk or thunderbird junk controls. In the 'Spam' folder, look at the 'Junk' column: if the email has a grey outline of a flame then email was put in the Spam folder by the server. if the email has a red/orange coloured flame icon, then it was put there by Thunderbird. If using a Pop account then only thunderbird can put the emails in the 'Junk' folder because any emails the server put into the server Spam folder cannot be accessed nor seen in Thunderbird. Have you set up the Thunderbird junk controls for each mail account ? * Menu icon > Account Settings * select 'Junk Settings' for the mail account. * select 'Enable adaptive junk mail controls for this account' * Select any of your address books to act as Whitelists. So Thunderbird is told to trust any contact email address in any of the selected address books. Regarding :'Trust junk mail headers set by SpamAssassin' Only select that option if you want to accept any setting that has been set by the server. * select 'Move new junk messages to' '''If POP:''' * select 'Junk folder on and choose the mail account name email address' '''IF IMAP''': * select 'Other' and choose 'Spam' folder on imap mail account' * click on 'OK' At this point, if you have not already set up the global settings do this: * click on 'Global Junk Preferences' button It opens in a new tab Suggest you select the following: * Select : 'When I mark messages as junk: * Select : 'Move them to the accounts 'Junk' folder' * Select : 'Enable adaptive junk filter logging' (this may prove useful) Training the Junk Controls involves you selecting what is Junk and also what is Not Junk. Access the Junk/Spam folder For any email which is Not Junk. If Thunderbird set it as Junk - has red/organge flame please select the email so it displays in the Message Pane and then click on 'Not Junk' button. Email should get moved back to Inbox. For any email set as junk by server - has grey outline flame Right click on email in Message List and select 'Mark as > Not Junk' Please note as these emails are being put in Spam by the server, you will need to make a note of the email address and then logon to your webmail account and set up the Spam settings. You may need to set an allow this email address/contact filter to stop the server putting email in Spam folder.