Although the complexity of the immune system is out of the question, the practical applications of vaccinology are often based on simplistic strategies based on "linear" thinking. In this paper the basic mechanisms of infection defenses are highlighted, paying particular attention to the molecular mechanisms of influenza virus antigens recognition. By identifying some types of antibodies against hemagglutinin, the molecular basis of autoimmunity to these antigens has also begun to be understood. Autoimmunity, in general, can be induced by infections in particular predisposed subjects, but it can also be a rare consequence of vaccination, due to the interaction between specific antigens, nonspecific adjuvants, macrophages and immune system. The complexity in vaccinology derives from many factors, related to the actual vaccination intervention (vaccine efficacy, coverage, herd effect) or emerging from the very use of large-scale vaccines (appearance of resistant strains, vaccinated people as carriers, shift of disease onset at adult age, concerns for adverse events). Identifying the critical points that still hinder a unanimous opinion on the various vaccines is the premise to promote their more effective use and to direct research towards objectives useful for this purpose.
Keywords: Complex systems, Biological defenses, Influenza, Autoimmunity, Adjuvants, Vaccinations.