Programs for vaccination against the new influenza A/H1N1 targeting many hundred million citizens in Europe and the USA are to be launched in the fall of this year. The USA is planning to employ a non-adjuvanted vaccine, whereas European nations are opting for inclusion of MF59, the adjuvant contained in an alternative seasonal flu vaccine, or the related adjuvant AS03 that is contained in a recently developed H5N1 vaccine. We draw attention to unappreciated hazards of using adjuvanted vaccine in Europe. Evidence from animal experiments in conjunction with clinical epidemiological data indicates that, quite irrespective of cause, stimulation of the immune system may accelerate atherogenesis. Application of adjuvanted flu vaccines to individuals at risk may therefore aggravate the course of underlying atherosclerotic vessel disease with all the clinical consequences. The same may hold true for other widespread diseases that are propelled by deregulated immune mechanisms. Safety trials conducted to date have not specifically taken these possible side effects into account, and unexpected serious adverse effects thus may follow in the wake of a general vaccination program. A prudent consequence would be to establish careful survey systems alongside with mass application of new adjuvanted vaccines, or to hold mass vaccination in reserve for use only in situations of true need, such as would arise with the emergence of a more virulent new H1N1 virus strain, or to use non-adjuvanted vaccines in individuals who are potentially at risk for adverse side effects.