The present invention relates to the use of a preparation of an active enamel matrix substance, such as an amelogenin, for the manufacture of a pharmaceutical composition for modulating an immune response. The composition can be used in preventing and/or treating a condition or disease in a mammal that is characterised by said mammal presenting an imbalance in its native immune response to an internal and/or external stimuli, i.e. wherein at least a part of said mammal's immune system is stimulated non-discriminatingly, reacts hypersensitively to said immunogen, or fails to react to said stimuli. Said condition can typically either be systemic or local, such as a systemic and/or post-traumatic whole-body inflammation or an autoimmune disease.