Brain microdialysis is an analytical technique used for the dynamic monitoring of brain neurochemistry in awake, freely moving animals. This technique requires the insertion of a small dialysis catheter, called a microdialysis probe, into a specific brain region, and its perfusion with an artificial extracellular fluid. The microdialysate samples, obtained from the probe outlet, can be analysed using high-performance liquid chromatography with electrochemical detection for the quantification of oxidizable molecules recovered from the extracellular space. In this chapter, we describe a protocol for performing a microdialysis setup and experiment in freely moving rats and mice. Furthermore, the high-performance liquid chromatographic determination of ascorbic acid, uric acid, catecholamines, indolamines and derivatives is described in detail.