Mucosal inflammation is associated with altered expression of cell membrane molecules. Disaggregation of tissue for flow cytometry may introduce artefactual changes. In an attempt to prevent the induction of artefacts, cells were fixed prior to isolation. The addition of 0.1% buffered formaldehyde to the collagenase/dispase digestion of mucosal biopsy specimens from patients with inflammatory bowel disease enhances detection of CD3, CD11b, CD16, CD63, and CD14. No significant effect was noted for CD19, CD67 or CD45. The expression of CD3, CD11b and CD45 correlated with the degree of endoscopic inflammation. Dilute buffered formaldehyde may be a useful adjunct to the enzymatic isolation of cells from mucosal specimens, by protecting surface antigens from digestion or alterations in expression.