AbstractBoraginaceous plants are characterized by high levels of polyunsaturated fatty acids and show a high ratio of ω‐3/ω‐6 fatty acids. In addition, Lappula squarrosa (Boraginaceae) shows high levels of stearidonic acid content (ω‐3; 18:4; 6,9,12,15‐octadecatetraenoic acid) showing interesting medical and health promoting properties. On the other hand Boraginaceous plants contain genotoxic and carcinogenic pyrrolizidine alkaloids (PA). An HPLC–ESI–MS/MS sum parameter method was developed to monitor the total sum of 1,2‐unsaturated PA in seed oil. The method was used to monitor different steps in oil refinement using lab model experiments and pilot scale refinement of L. squarrosa seed oil. A limit of detection and a limit of quantification (LOQ) of 0.02 μg retronecine equivalents (RE)/kg and 0.05 μg RE/kg were achieved, respectively. Multiple washing steps at pH 2.2 can significantly reduce the PA content to 0.07 % of the start value. In addition, combining washing with neutralization, bleaching and deodorization can reduce the PA content of L. squarrosa oil below the LOQ (0.05 μg RE/kg). The newly established method was further used to analyze the PA content of commercially available Boraginaceous seed oils (Echium spp., Borago officinalis). Three out of ten products were tested as PA positive (PA content ranging from not detected to 0.6 μg RE/kg product).