A capillary zone electrophoretic (CZE) method is described for the analysis of the raffinose family of oligosaccharides (RFO) in pea seeds. Extraction of RFO was carried out in 80% ethanol and the extract was passed through a Sep-Pak C18 cartridge. This proved to be an improvement on the currently accepted purification technique. High-quality electrophoregrams were obtained which allowed the separation and quantitation of sucrose, raffinose, stachyose and verbascose The CZE results were compared with those obtained by anion-exchange high-performance liquid chromatography coupled to a triple-pulsed amperometric detection (HPAC-PAD). The samples were obtained from four pea strains which were near-isogenic except for genes at the r and rb loci. A high degree of precision and reproducibility was obtained for the RFO compositions of all the pea strains. No statistically significant differences (p < or equal to 0.05) were found between the two analytical techniques using paired Student-t tests.