Abstract: Biomarkers associated with inflammatory bowel disease (IBD) are provided, as well as methods of using such biomarkers for diagnosing, assessing and monitoring disease progression. The biomarkers may be measured at the protein level or the gene expression level Biomarkers may be tracked individually or in groups of two or more. The disclosed biomarkers may find particular utility in monitoring a course of therapy, such as treatment with an IL-23 antagonist. Changes in biomarker levels can also be used to confirm target engagement and therapeutic efficacy. Changes in biomarkers can also be used inform modification of a therapeutic regimen, for example to increase or decrease dosing of a therapeutic agent, such as an anti-IL-23 or anti-IL-23R anti-body.