A sensitive method for the measurement of endogenous 5-methoxytryptamine in brain tissue has been developed using capillary column gas chromatography-electron-capture negative-ion chemical ionization mass spectrometry. 5-Methoxytryptamine was first converted to N-[2H3]acetyl-5-methoxytryptamine by reaction with hexa-deuterated acetic anhydride, followed by reaction with pentafluoropropionic anhydride to yield the highly electron-capturing 3,3'-spirocyclic pentafluoro-propionyl indolenine derivative. Quantitative analysis was carried out by selected-ion monitoring of the [M-HF].- and [M-HF-DF].- ion intensity of the 3.3'-spirocyclic pentafluoropropionyl indolenine derivative, using 5-methoxy-[alpha, alpha, beta, beta-2H4]tryptamine as the internal standard. The presence of 5-methoxytryptamine in the brain tissue was demonstrated. In the absence of a monoamine oxidase inhibitor, the mean +/- S.D. levels of 5-methoxytryptamine in the rat and quail whole brain were found to be 30 +/- 6 and 347 +/- 52 pg/g, respectively. The possible physiological functions of 5-methoxytryptamine as a neuromodulator and/or neurotransmitter have to be considered.