M cells represent an important gateway for the intestinal immune system by delivering luminal antigens through the follicle-associated epithelium to the underlying immune cells. The goal of this study was to characterize this route of antigen uptake during intestinal inflammation by characterizing M cell formation and M cell-associated lymphocytes after indomethacin challenge in rats. We demonstrated increased M cell formation as early as 12 h after a single injection of indomethacin. The elevated M cell counts were determined until day 3 and returned to basal levels after 7 days. Electron microscopic studies revealed an expansion of mononuclear cells inside the M cell pocket that were characterized predominantly as B cells, T cell receptor (TCR)alphabeta- and CD4-positive T cells, whereas other markers such as CD11b, CD8 and CD25 remained unchanged. In situ hybridization studies showed increased expression of interleukin (IL)-4 by lymphocytes during intestinal inflammation in the Peyer's patch follicle. These studies illuminate the relevance of M cells during intestinal inflammation and suggest that M cells derive from epithelial cells in a certain microenvironment.