The presence of pyrogens in the human body can activate the immune system leading to pathological effects, such as fever, tissue damage, septic shock, possibly even death. This is a major concern in the pharmaceutical field where injectable solutions are widely used. The main pyrogens are the lipopolysaccharide (LPS) molecules from Gram‐negative bacteria and the lipoteichoic acid (LTA) from Gram‐positive bacteria. Conventional sterilization methods cannot fully inactivate these molecules. A significant decrease of the pyrogenic activity of both LPS and LTA is obtained after exposure to the flowing afterglow of a N2–O2 discharge. We also investigated the level of pyrogenic activity ensuing from the inactivation of bacterial spores by the flowing afterglow.