Abstract We used two-dimensional difference in-gel electrophoresis (2-D-DIGE) for proteome analysis of cerebrospinal fluid (CSF) in Guillain–Barré syndrome (GBS). Spots showing > 2-fold difference between GBS and controls were analysed using MALDI-TOF mass spectrometry. Proteins that were up-regulated in GBS included haptoglobin, serine/threonine kinase 10, α-1-antitrypsin, SNC73, alpha II spectrin, IgG kappa chain and cathepsin D preprotein, while transferrin, caldesmon, GALT, human heat shock protein 70, amyloidosis patient HL-heart-peptide 127aa and transthyretin were down-regulated. Some of these proteins are reported in CSF of GBS for the first time. Accordingly, the 2-D-DIGE technology may be useful to identify disease-specific proteins in patients with GBS.