Inflammatory rheumatic diseases with their unclear aetiology are a challenge for the routine clinical practice. The dominating inflammatory processes with many facets of autoimmune phenomena have been extensively studied during the last decades. Modern high throughput technologies provide for the first time the opportunity to obtain an insight into the many different molecular aspects in one patient in parallel. Step by step, concepts can be developed to understand the relationships and interdependencies of the molecular processes and to place them in order of importance for each individual separately. Thus, studies have demonstrated that the risk of disease severity can be estimated and the response to therapy can be objectified based on molecular investigations. Exemplarily, the potential has been demonstrated that the therapeutic outcome towards a defined treatment may be predicted. Despite the high cost, it is becoming more and more obvious that an extensive increase of knowledge depends on the detection of a multitude of parameters, a task which will need to be accomplished in the near future.