In the past decade, infectious diseases in the cardiovascular sector have been increasingly emerging as a clinical challenge. This is not only to be attributed to an increasing pathogen-specific resistance to chemotherapy but also to an improved therapy landscape, such as implanting cardiac pacemakers, heart valve systems and artificial heart systems. Current research results show that a polymicrobial pathogen infiltration defines the disease status and course. Previous research efforts focused on identifying pathogen spectra by means of total genome investigations. Further, the goal of the research effort is to identify disease-causing pathomechanisms. To this end, it is necessary to ensure the identification agents up to the root level to allow conclusions on disease mechanisms. Initially, the microbial community of a patient sample was analyzed via a specifically defined PCR panel. The PCR allows a quick analysis of known pathogenic germs. As unknown bacteria, which may also be pathogenic, remained undetected, the T-RLFP analysis was also used to characterise the diversity of the samples. This non-targeted method is based on the amplification and restriction of 16S RDNA and then uncovers unknown germs via cloning and sequencing. However, the sensitivity of the method is limited by the number of clones analyzed, and in some cases it does not read a differentiation of the species of a genus. A more sensitive process is genome sequencing based on the 16S RDNA or the overall genome. It was possible analyse the microbial composition of a patient sample and also detect bacteria in low concentrations up to the species level. The main challenge in applying the new analysis methods lies at the level of bioinformatics diagnostic strategies. This ranges from the assignment of pathogen-specific DNA molecules to the identification of the pathogen stem to the classification of virulence factors. These virulence factors must be correlated with the patient outcome in prospective clinical trials and thus their clinical relevance will be developed. The aim of the working group is to develop this clinical molecular biological diagnostic path, to establish necessary bioinformatic tools and to incorporate the findings into the daily routine in clinics.