Numerous investigations have demonstrated efficiencies of different disinfection methods, but until now only little is known about long-term effects on community compositions of drinking water biofilms. Changes in the community structure, especially regrowth of hygienically relevant microorganisms could be critical for the drinking water quality. In this study the long-term effect of disinfection methods on biofilm communities in drinking water systems was analysed. Old drinking water biofilms grown in silicone tubes were exposed to different preparations of disinfectants (free chlorine, chlorine dioxide, hydrogen peroxide combined with fruit acid, silver and silver with peracetic acid, respectively) and subsequently further exposed in the original drinking water. The comparison of the treated and regrown biofilm populations with untreated ones by the DNA-fingerprinting method denaturing gradient gel electrophoresis (DGGE) revealed a considerable population shift caused by the disinfectants. The disinfection methods induced a selection pressure on the biofilm populations depending on the composition and concentrations. The similarities between the treated and untreated biofilms were generally low. Compared to preparations with peracetic acid the disinfection with hydrogen peroxide and silver resulted in higher similarities of the treated and untreated biofilms, but the microbial diversity increased. It can be concluded that the disinfectants have a major impact on the drinking water biofilm communities and that possibly the intervention selects persisters and microorganisms, which can live on the residuals of the dead biofilm cells. For the evaluation of the efficiency of disinfection methods in drinking water installations it is necessary not only to consider reduction of certain bacteria but also to pay attention to the biofilm community.