In the past decade microdialysis has become a method of choice in the study of unbound tissue concentrations of both endogenous and exogenous substances. Microdialysis has been shown to offer information about substances directly at the site of action while being well tolerable and safe. The large variety of its field of application has been demonstrated. However, a few challenges have to be met to make this method generally applicable in routine applications. This review will provide an overview over theoretical aspects that have to be considered during the implementation of microdialysis. Moreover, a comparison between microdialysis and other tissue sampling techniques will demonstrate advantages and limitations of the methods mentioned. Subsequently, it will present a critical synopsis of a variety of scientific/biomedical applications of this method with emphasis on the most recent literature, focussing on target tissues while giving examples of substances examined. It is concluded that microdialysis will be of great value in future investigations of pharmacokinetics, pharmacodynamics and in monitoring of disease status and progression.