SUMMARYBackground: Most array analyses of ulcerative colitis have focused on identifying susceptibility genes for ulcerative colitis. Aim: To clarify the changes in gene expression during inflammation in ulcerative colitis colon mucosa using cDNA macroarray. Methods: From 23 ulcerative colitis patients, 16 each of inflamed and non-inflamed specimens (total 32 samples for individual analysis) were obtained by colonoscopic biopsy. Eighteen of the 32 samples, used for pairwise analysis, consisted of nine sample pairs, each pair being from the same patient. We examined expression profiles of approximately 1300 genes with cDNA macroarray.