Thunderbird's internal filtering will identify what it thinks is Junk. Your email provider is categorizing what they think is spam, and apparently are putting this into a Spam folder. Spam and Junk are separate and distinct from one another. Thunderbird needs to be trained to accurately identify Junk. You need to mark junk mail as "Junk", and check over what is in the Junk folder or has been marked as Junk, and if any good messages have been incorrectly classified as Junk, you need to mark them as "Not Junk". Messages moved directly to the Spam folder by your email provider won't ever appear in the Inbox and so will miss being classified by the Junk controls. You can hasten your Thunderbird's training by looking over your Spam folder, making sure everything in it should be there. (If you have messages incorrectly categorized as Spam, you need to find out how your email provider can allow you to teach it that they are good messages.) When you're happy that all the messages are genuinely Spam, mark them as Junk (select all, hit j) thus reinforcing Thunderbird's Junk Controls' idea of what a bad message looks like. Now, can you explain what this filter you have set up is designed to do?