The cholinergic system is an important modulatory neurotransmitter system in the brain. Changes in acetylcholine concentration have been previously determined directly in animal models and human brain biopsy specimens, and indirectly, by the effects of drugs, in living humans. Here, we developed a method for direct determination of acetylcholine synthesis in living brain tissue. The method is based on administration of choline, enriched with carbon-13 (stable isotope) in the two methylene positions, and detection of labeled acetylcholine and all other metabolic fates of choline, by carbon-13 magnetic resonance spectroscopy. We tested this method in rat brain slices and found it to be specific for acetylcholine synthesis in both the cortex and hippocampus. This method is potentially useful as a research tool for exploring the cholinergic system role in cognitive processes and memory storage as well as in diseases in which the malfunction of the cholinergic system has been implicated.