Microdialysis is a dynamically evolving method utilized for monitoring of tissue metabolism and barrier function, pharmacological studies and to estimate local blood perfusion in situ. The present review summarizes current knowledge of the last of the aforementioned applications on a characterization and comparison of two approaches used - microdialysis flow-indicator dilution technique and continuous metabolic monitoring. Currently, the use of metabolic indicators, which enable sensitive and complex evaluation of perfusion-induced changes in the tissue, is preferred. Despite the methods numerous advantages the measurement of tissue blood perfusion by microdialysis remains centralized in the area of clinical research, for the present. For wider acceptance and exercise in the routine clinical practice, more validating studies ought to be conducted and situations identified, where microdialysis could replace the current methods.