Background Crohns disease (CD) 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 CD disease.Methods Surgery biopsies (n=60) were sampled at consecutive active involved and uninvolved sites at the same time in individual CD 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.