A simple and sensitive method has been developed for the rapid qualitative and quantitative analysis of the phytotoxins produced by Ascochyta caulina, a potential mycoherbicide for the biocontrol of Chenopodium album. Considering that the two main toxins produced by this fungus, namely ascaulitoxin and trans-4-amino-D-proline, and the third toxin, identified as 2,4,7-triamino-5-hydroxyoctandioic acid, have an amino acid nature, high-performance anion exchange chromatography with pulsed amperometric detection was the best method for their detection. The method was used to measure the toxin content in the culture filtrates of different strains of A. caulina. The developed method could be employed as a tool to select more virulent strains by determining the higher toxin producers, if in vitro toxin accumulation was related to pathogen virulence. The chemical characterisation of the third toxin purified from A. caulina culture filtrates is also reported.