The drinking water distribution system of a hospital was investigated using standard cultivation techniques, taxon-specific PCRs targeting pathogenic bacteria, denaturing gradient gel electrophoresis, cloning and sequencing. The results obtained verify the higher sensitivity of PCR compared to cultivation for detecting Legionella and Pseudomonas aeruginosa. Moreover, several other opportunistic pathogenic bacteria, such as Escherichia albertii, Acinetobacter lwoffi and Corynebacterium tuberculostrearicum, were detected, emphasizing that drinking water systems, especially those with stagnant water sections, could be the source of nosocomial infections.