The complex inflammatory bowel diseases, Crohn’s Disease (CD) and Ulcerative Colitis (UC), are driven by a myriad of immune, microbial, and environmental factors that manifest in tissue inflammation and lesions. Though several mouse models exist for studying these disorders, a quantitative assessment of the correspondence of different IBD mouse models to UC and CD is needed. Here, we perform a comparative transcriptomic analysis of established IBD mouse models with human IBD patient cohorts using publicly available transcriptomic datasets to identify the most representative mouse models of CD and UC phenotypes.