The implied aetiological association of measles virus with Crohn's disease would be supported by detection of an immune response to infected cells in affected tissues. This study sought to detect and characterise in situ immune responses to measles virus in both acutely and persistently infected tissues, and in particular, Crohn's granulomata. Tissue sections from patients with Crohn's disease (n = 17), tuberculosis (n = 9), acute intestinal ischaemia (n = 5), acute measles pneumonitis (n = 2), acute measles appendicitis (n = 1), subacute sclerosing panencephalitis (SSPE; n = 1), and measles inclusion body encephalitis (MIBE; n = 1), were examined. Single and double immunohistochemical labelling was performed to identify both cytotoxic lymphocytes (CD8, TIA, perforin, Leu 7, CD45RO, CD45RA) and macrophages (KP1). The relationship of these cells to measles infected cells was examined by double immunolabelling with antimeasles virus nucleoprotein antibody. In both acute measles appendicitis and SSPE, CD8+/TIA cytotoxic lymphocytes (CTL) targeted infected cells. In the cases of Crohn's disease (13/17), MIBE, fatal pneumonitis, and one tuberculous granuloma, that were positive for measles virus, infected cells appeared to be targeted by macrophages rather than CTL. CTL in both tuberculous and Crohn's granulomata were similar in their peripheral distribution, number, and phenotype. The data suggest that measles-specific CTL responses may be attenuated in Crohn's disease compared with acute measles appendicitis and SSPE, and secondly, that an abnormal macrophage response to persistent measles virus infection of the intestine may result in granulomatous inflammation.