Anthrax spores enter the respiratory system when they are inhaled through the nose or mouth. Larger spores may settle in the windpipe (trachea). The immune system reacts by trying to destroy the spores. Some spores may escape and travel to the lymph nodes located in the chest. Smaller spores travel farther down the respiratory tract and invade tiny air sacs (alveoli) in the lungs, where the spores germinate and cause an active bacterial infection.

The anthrax bacteria start multiplying within 1 to 60 days. After the bacteria infect chest tissue, the disease rapidly progresses. Toxins from the bacteria enter the bloodstream and spread throughout the body, causing severe damage to tissue, lungs, and other organs. The infection is difficult to treat after it enters the bloodstream.