This report describes a method for assay of choline (Ch) and acetylcholine (ACh) levels in rodent brain regions by high-performance liquid chromatography combined with continuous-flow fast atom bombardment mass spectrometry. Following an investigation of various extraction procedures and chromatographic conditions, we found that homogenization in acetonitrile in the presence of magnesium sulphate followed by heptane extraction and then a flow rate programme for chromatographic separation yielded the best results of the protocols tested. Under these conditions, the recoveries of Ch and ACh were 75% and 80%, respectively, with detection limits of 5 pmol for Ch and 2 pmol for ACh. Using this method, Ch and ACh levels in rat and mouse brain regions were similar to those reported by other researchers.