Capillary liquid chromatography–mass spectrometry (cLC–MS) was coupled on-line to microdialysis sampling to monitor endogenous acetylcholine (ACh) from the rodent brain. In vivo microdialysate sampled at 0.6μL/min from the striatum of ketamine or chloral hydrate anesthetized rats was loaded onto a sample loop and then injected onto a ∼5cm long strong cation exchange (SCX) capillary column. A step gradient was used to separate the analyte from ionization suppressing salts contained in dialysate in 2.4min. Sampling coupled on-line with cLC–MS allowed for high temporal resolution (data points at 2.4min intervals), good reproducibility (10–15% relative standard deviation, R.S.D.), and sensitive limits of detection (0.04nM or 8amol injected). The method successfully monitored basal and stimulated levels (induced by increased K + concentrations) of ACh from the anesthetized rat without necessitating perfusion of an acetylcholinesterase (AChE) inhibitor. Absolute and percent basal levels of ACh from rats receiving different anesthetics were also compared.