Microdialysis is an important in vivo sampling technique, which is useful in both pre-clinical and clinical applications, and has been widely used in neuroscience research. The in vivo microdialysis technique is coupled with high performance liquid chromatography (HPLC) and mass spectrometry (MS) to allow for measurement of the extracellular levels of various neurotransmitters such as acetycholine (ACh), dopamine (DA), norepinephrine (NE) and serotonin (5-HT), glutamate (Glu), and gamma aminobutyric acid (GABA), as well as the metabolites of the neurotransmitters, and various neuropeptides in discrete brain regions of laboratory animals. Although this approach lacks the temporal and spatial resolution of FSCV, HPLC-MS offers a reliable way to identify and measure the absolute levels of various neurotransmitters in vivo.