Autoantibodies against heat shock protein 40 (HSP40) and their clinical significance in ulcerative colitis (UC) have not been evaluated before. Twenty-six tissue specimens of inflamed areas from patients with UC, 16 from patients with Crohn's disease (CD) and 16 endoscopically normal tissues were analysed for HSP40 expression. Sera from 47 patients with UC and 44 healthy volunteers were examined for the presence of autoantibodies against HSP40 by enzyme-linked immunosorbent assay test. Immunohistochemistry showed that 17 out of 26 specimens from UC patients, one specimen from a CD patient and one normal tissue specimen were positive for HSP40. Most HSP40-positive cells expressed CD68. Higher titres of anti-HSP40 autoantibodies were detected in sera from UC patients compared with healthy volunteers. In patients with inactive disease, those with proctitis or left-sided colitis had higher titres of anti-HSP40 autoantibodies than those with total colitis. Our study suggests that autoimmunity against HSP40 may have a beneficial effect in UC patients by limiting the extent of the disease.