Background Ulcerative colitis (UC), is a chronic, relapsing, and debilitating idiopathic inflammation, with variable and complex pathophysiologies.Our objective was to elucidate patterns of gene expression underlying the progression of UC disease.Methods Single endoscopic pinch biopsies (n=41) were sampled at both active and inactive stages at the same site in individual UC patients and compared with each other and to non-IBD healthy controls.Gene expression results were validated by quantitative reverse transcriptase-PCR (QRT-PCR), and results at the protein level were validated by immunohistochemistry and western blot.