Dencichine (β-N-oxalyl-l-α,β-diaminopropionic acid) is a haemostatic agent present in well-known traditional Chinese medicinal herbs such as Panax notoginseng, as well as other Panax species. It is also a reported neurotoxic agent found in Lathyrus sativus (grass pea seed) and cycad seeds. A method was developed for quantitative determination of the non-protein amino acid, dencichine, in plant samples of P. notoginseng and the adventitious roots directly from the explants of P. notoginseng after derivatization with ethyl chloroformate (ECF) by gas chromatography–mass spectrometry (GC–MS). l-2-chlorophenylalanine was used as an internal standard. Calibration curves were linear (r2 = 0.9988, n = 6) in the range of 10–800 μg/ml for dencichine. Limit of detection and quantification for dencichine were 0.5 μg/ml and 2 μg/ml, respectively. This rapid and specific method may be applied to the quantification of dencichine in complex medicinal plants and their products.