Increasing availability of high throughput technologies, exponentially growing information about the human genome and gene expression, and the growing global network of databases on systematic biomedical information will change our view on inflammatory rheumatic diseases in a revolutionary way. Several research laboratories have already generated initial extensive datasets on gene expression analysis. Application of this technique has demonstrated that in addition to a precise analysis, verification and validation of the results also on the level of cell populations, a meticulous characterization of the patients according to current conventional clinical, laboratory, imaging and histological standards is essential. For functional interpretation, in vitro tests, animal models and therapeutic studies will provide further information. Bioinformatic structuring and development is needed for the large amounts of data. After an initial genome-wide screening, the objective is to identify those genes, which will allow characterization of the disease, classification according to molecular pathophysiology, evaluation of the prognosis and prediction of the correct and most potent therapeutic regimen. Derived from the improved knowledge about the molecular mechanisms, new and--as to expect--the crucial approaches for an effective therapy against chronic inflammation, organ destruction and pathological immune response in rheumatic diseases will emerge.