The proteomes and glucosinolate content of two commercial rapeseed meals produced by cold-pressing and pre-press solvent extraction were investigated with the aim of identifying process-related differences between them. One-dimensional protein electrophoresis of the meals and their corresponding protein isolates revealed similarities in protein band distribution between cold-pressed and pre-press solvent extracted samples. Two-dimensional protein electrophoresis coupled with mass spectrometry confirmed that the seed storage protein cruciferin was the major protein in both meals either intact or in the form of α- and β- polypeptide subunits. HPLC analysis indicated that cold-press meals contained significantly higher amounts of glucosinolates than the solvent-extracted meals. Progoitrin was the main glucosinolate detected irrespective of the processing method used for extraction and levelled to 2.52 g/kg and 1.25 g/kg for cold-pressed and solvent–extracted meal respectively. Furthermore, glucosinolate-free protein isolates were prepared from this by-product of the oil production industry.