Numerous studies in the past decade have identified N-β-methylamino-L-alanine (BMAA) as a putative environmental neurotoxin. Produced by cyanobacteria and accumulated at different levels of the trophic system, BMAA has been detected in the brain tissue of human patients that died from progressive neurodegenerative disease. Research into the mechanism of neurotoxicity has been hampered by conflicting results and disagreement in the literature over analytical methods used for quantification and detection. While several research approaches have been tested, the use of the derivatizing reagent 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate is presented here as an effective and selective means for the analysis of BMAA and two co-occurring biological isomers, DAB and AEG, by liquid chromatography and tandem mass spectrometry.