We recently described cobblestone (Cob) lesions in the ileum of SAMP1/YitFc (SAMP) mice, which is the only inbred mouse strain with polygenic predisposition to Crohn’s disease(CD)-like ileitis. Herein, we quantified the mRNA gene expression differences across microscopically dissected samples from ileal tissues of adult germ-free (GF)-SAMP mice.