Since the discovery of diphtheria toxin inactivation in the early 1920s, formaldehyde has been used to inactivate bacterial toxins and viruses used as vaccine antigens. More recently, formaldehyde was used to inactivate pertussis toxin (PT), a component of the newly developed diphtheria-tetanus-acellular pertussis (DTaP) vaccine. This application however illustrated the complexity of the reaction. To eliminate the need for inactivation, the mutant PT-9K/129G was developed. This toxin analogue is irreversibly devoid of toxicity and is a more immunogenic antigen than chemically detoxified PT. Native antigens however proved less stable than detoxified antigens upon storage or heating. We investigated the use of low concentrations of formaldehyde as a stabilizing agent for PT-9K/129G. Under the conditions selected, its antigenic characteristics were retained. Enhanced immunogenicity compared to detoxified preparations was demonstrated in clinical trials in infants where DTaP vaccines containing formalin-stabilized PT-9K/129G were compared to other DTaP vaccines containing detoxified wild type PT. Additional studies with filamentous haemagglutinin (FHA), another component of acellular pertussis vaccines, showed how high formaldehyde concentrations could depress the presentation of epitopes to T-cells by limiting the antigen processing. In conclusion, mild formaldehyde treatment can be applied to stabilize vaccine antigens while retaining optimum antigenic activity.