Capillary zone electrophoresis with mass spectrometry (CE-MS) and UV detection (CE-UV) was applied to the quantitative determination of gamma-glutamyl-S-ethenyl-cysteine (GEC), a bioactive and unstable compound present in Vicia narbonensis L. seeds. This compound is responsible for, among other negative effects, palatability reduction and grain toxicity. In order to carry out the quantitative analysis of GEC, different conditions (such as composition, concentration and pH of the background electrolyte, and type and time of extraction) were studied. Also, adequate conditions for electrospraymass spectrometry of this bioactive compound were investigated. The best extraction conditions of GEC from V narbonensis L. seeds flour were obtained using ethanolwater (70:30 v/v) for 45 min. The use of a 20 m ammonium hydrogen carbonate at pH 7 provided adequate analytical conditions compatible with the unstable nature of GEC as well as with the requirements of CE-UV and CE-MS analysis. A comparative study was carried out between the different figures of merit of CE-UV and CE-MS for quantitative purposes. Both techniques provided similar limit of detection and can be applied with confidence within the same linear dynamic range. However, reproducibility and speed of analysis were better using CE-UV. The developed methods were readily applied to quantify GEC in seeds of 21 genotypes of V narbonensis L.. A good agreement between CE-MS and CE-UV results was observed corroborating the usefulness of both approaches for quantitative purposes.