After a nosocomial outbreak caused by Legionella pneumophila serogroup 5, the hospital water distribution system, which was found to be colonized by L. pneumophila serogroups 5 and 6, was decontaminated by the superheat and flush method and by installing an additional heat-shock unit in one of the hot water circuits. This unit exposed the recirculated water to a temperature of 80 degrees C. The efficacy of the decontamination measures was evaluated by monitoring the temperatures and legionella concentrations at different parts of the hot water distribution system. The genetic diversity of the colonizing legionella flora was examined using two genotyping methods: amplified fragment length polymorphism analysis (AFLP) and random amplified polymorphic DNA (RAPD) analysis. Selected serogroup 6 strains were also analyzed by sequence-based typing (SBT). The results indicated that long-term eradication of serogroup 5 strains was never achieved. Only one serogroup 6 strain was never isolated after the superheat and flush. In all, according to genetic fingerprints, the diversity of Legionella strains in a hospital water system remains stable over the years regardless of the use of recommended disinfection procedures.