AIMS: To determine the specificity of persistent measles virus infection in intestinal samples from Crohn's disease patients using quantitative immunogold electron microscopy. To compare the results with samples from ulcerative colitis, a granulomatous inflammatory control (tuberculous lymphadenitis), and a positive control. METHODS: Formalin fixed, paraffin embedded intestinal tissue from patients with Crohn's disease was reprocessed and stained with antimeasles nucleocaspid protein primary antibody followed by 10 nm gold conjugated secondary antibody. Tissue samples were taken from granulomatous and non-granulomatous areas of the intestine. Intestinal samples from patients with ulcerative colitis, tuberculous lymphadenitis, or acute mesenteric ischaemia were similarly processed. Brain tissue from a patient with subacute sclerosing panencephalitis (SSPE) was used as the positive control. Duplicate sections of all tissues were processed without the primary antibody. Stained specimens were examined by electron microscopy. RESULTS: In Crohn's disease patients, 8/9 foci of granulomatous inflammation and 0/4 foci of non-specific inflammation were positive for measles virus. Of controls, 0/5 non-inflamed intestinal tissues, 1/8 tuberculous tissues, 1/5 ulcerative colitis tissues, and 1/1 SSPE tissues were positive. Gold grain counts per nuclear field-of-view in both Crohn's disease granulomas (43.29) and SSPE (36.94) were significantly higher than in tissues from patients with ulcerative colitis (13.52) or tuberculous lymphadenitis (15.875), and nongranulomatous areas of Crohn's disease (4.89) (p < 0.001, p < 0.001, p = 0.0006, respectively), with no significant difference between Crohn's disease and SSPE (p > 0.1). In both SSPE and Crohn's disease staining was confined to a small population of cells exhibiting characteristic cytopathology. CONCLUSION: These data support a role for measles virus in the aetiology of Crohn's disease.