Microdialysis is currently optimized to sample the extrasynaptic pool. As such, the technique has facilitated discovery of ischemia-induced excitotoxic glutamate overflow (Benveniste H, Drejer J, Schousboe A, Diemer NH, 1987, Regional cerebral glucose phosphorylation and blood flow after insertion of a microdialysis fiber through the dorsal hippocampus in the rat. J. Neurochem., 49, 729–734) and adenosinergic sleep drive (Porkka-Heiskanen T, Strecker RE, Thakkar M, Bjorkum AA, Greene RW, McCarley RW, 1997, Adenosine: a mediator of the sleep-inducing effects of prolonged wakefulness. Science, 276 (5316), 1265–1268); and is proving essential for clinical monitoring of glutamate and cellular metabolites in stroke and head trauma (Sarrafzadeh AS, Sakowitz OW, Kiening KL, Benndorf G, Lanksch WR, Unterberg AW. Bedside microdialysis: a tool to monitor cerebral metabolism in subarachnoid hemorrhage patients? Crit. Care Med. 2002, 30 (5): 1062–1070). Study of the origin of extrasynaptic glutamate sampled with microdialysis has advanced understanding of extrasynaptic signal processing (Baker DA, Xi ZX, Shen H, Swanson CJ, Kalivas PW. The origin and neuronal function of in vivo nonsynaptic glutamate. J. Neurosci. 2002, 22 (20): 9134–9141; Baker DA, McFarland K, Lake RW, Shen H, Tang XC, Toda S, Kalivas PW, 2003, Neuroadaptations in cystine-glutamate exchange underlie cocaine relapse. Nat. Neurosci., 6, 743–749) in the CNS. Microdialysis studies furthermore demonstrate that synaptic pools of some neurotransmitters spill into the extrasynaptic space. For this reason, microdialysis has provided a window into the synaptic pool that has significantly advanced understanding of neurotransmitter control of behavior (Tanda G, Pontieri FE, Di Chiara G, 1997, Cannabinoid and heroin activation of mesolimbic dopamine transmission by a common mu1 opioid receptor mechanism. Science, 276, 2048–2050). Nonetheless, ability to sample synaptic pools of neurotransmitters is limited. Here we summarize evidence that microdialysis often fails to sample synaptic pools of neurotransmitters, such as glutamate and GABA because of rapid clearance and limited diffusion of these neurotransmitters from the synapse. Moreover, we consider means to move the dialysis membrane closer to the synapse to facilitate sampling of the synaptic pool of these neurotransmitters by minimizing tissue trauma, decreasing probe size and increasing temporal resolution.