Methods and materials are disclosed for testing biomarkers in a subject suffering from inflammatory bowel disease (IBD) are described herein. Such detection can be useful for diagnosing and treating ulcerative colitis (UC) and Crohn's disease (CD), two forms of IBD that are otherwise difficult to distinguish. The method includes measuring the level of one or more of several biomarkers, including HD5 or MMP-7, which are expressed differentially in patents with UC and CD. A treatment may be based on the determination of whether the subject has ulcerative colitis or Crohn's disease.