To deal with the large amount of unsolicited email ("spam" or "junk mail") that most people have to cope with, Thunderbird uses an adaptive filter that learns from your actions which messages are legitimate and which are junk.
The filter is enabled by default. You can set system-wide preferences that determine what happens to messages marked as junk. These settings will be used by all your email accounts (although some settings can be overridden in the account settings, as shown below). To access the preferences, click Thunderbird > PreferencesTools > OptionsEdit > Preferences, select the Security panel and then select the Junk tab.
The configuration in the account preferences for each of your email accounts will override similar settings in the preferences described above. Click ToolsEdit > Account Settings and select Junk Settings in the left pane for the account to see these settings. This section includes the ability to enable addressbooks which will be used as a whitelist. If the sender of a message is a contact in an addressbook that has been enabled for whitelist, then that message will not be marked as junk.
In order for this filter to be effective, you must train it to recognize the messages that you consider to be junk and the messages that you consider to be not junk. So you will want to mark messages as junk, not delete them.
You can mark messages as junk by clicking in the "junk" column in the message list:
You can also mark messages as junk in the message pane by clicking the Junk button on the message header:
You can also use the small case j key to mark messages as junk.
You will need to mark many messages so that the adaptive filter has enough training data, including messages that are NOT junk. (more about that below)
It as just as important to tell the filter which messages are not junk.
First, during the early learning stages you will want to frequently, perhaps daily, check your Junk folder for messages that have been incorrectly classified as junk by clicking on the Not junk button, or using the upper case J on your keyboard. After the first week you should also check the junk folder for messages that are incorrectly marked as junk, perhaps weekly.
Secondly, very important, you will want to constantly train the filter by marking a quantity of GOOD messages as not junk, for example messages in your Inbox. You must use the keyboard upper case J, because there is no button - the "Not Junk" button appears only for messages that have already been classified as junk. Marking several messages per week will be sufficient. You can select many messages and mark them all at the same time. Note - unfortunately nothing in the user interface indicates whether a message has already been marked as "not junk".