<jats:title>Abstract</jats:title><jats:sec><jats:title>BACKGROUND</jats:title><jats:p><jats:italic>Lathyrus</jats:italic> species as legumes represent an alternative protein source for human and animal nutrition. Heavy consumption of these species can lead to lathyrism, caused by the non‐protein amino acid <jats:italic>β‐N</jats:italic>‐oxalyl‐<jats:sc>l</jats:sc>‐<jats:italic>α</jats:italic>,<jats:italic>β</jats:italic>‐diaminopropionic acid (<jats:italic>β</jats:italic>‐ODAP). Currently, there is no well‐defined level below which <jats:italic>β</jats:italic>‐ODAP is considered non‐toxic. In this work, the <jats:italic>β</jats:italic>‐ODAP content was determined in <jats:italic>L. sativus</jats:italic> and <jats:italic>L. cicera</jats:italic> samples to assess their potential toxicity. Homoarginine is another non‐protein amino acid found in <jats:italic>Lathyrus</jats:italic> spp. with interesting implications for human and animal nutrition.</jats:sec><jats:sec><jats:title>RESULTS</jats:title><jats:p>The level of <jats:italic>β</jats:italic>‐ODAP found in these two species ranged from 0.79 to 5.05 mg g<jats:sup>−1</jats:sup>. The homoarginine content of the samples ranged from 7.49 to 12.44 mg g<jats:sup>−1</jats:sup>.</jats:sec><jats:sec><jats:title>CONCLUSION</jats:title><jats:p>This paper describes an accurate, fast and sensitive method of simultaneous detection and quantification of <jats:italic>β</jats:italic>‐ODAP and homoarginine by capillary zone electrophoresis in <jats:italic>L. cicera</jats:italic> and <jats:italic>L. sativus</jats:italic> seeds. Moreover, several methods of extraction were compared to determine the highest performance. © 2014 Society of Chemical Industry</jats:sec>