Medicine is experiencing a period of change: Extensive molecular biological data on the patient are increasingly included in diagnosis and treatment. This trend is based on the development of targeted drugs and accompanying diagnostics, which serve the purpose of providing advance evidence that the medication promises therapy success for the patient. According to this concept drugs are often given in combination. The sizes of patient groups for which a given therapy out of many possible alternatives can be expected to be successful are quite limited. The relationship between the molecular data pertaining to a patient and their disease phenotype are complex and cannot be determined manually. Thus, computer-based bioinformatics methods play a central role in interpreting the molecular data and as an instrument for providing recommendations for the practicing physician. Bioinformatics is an essential component in basic research, in the development of new concepts for diagnosis and therapy as well as in clinical practice, in which these concepts are applied to treating patients. This article discusses the role of bioinformatics in both basic research and clinical practice. We present the example of treatment of HIV patients, for which bioinformatics-assisted therapy selection has already entered clinical practice. Such a therapy concept is also predestined for other diseases (e.g., cancer). The article concludes with remarks on the prerequisites for society as a whole for ensuring success of this concept of personalised medicine as a factor of medical progress.