The present invention provides methods for predicting the likelihood of mucosal healing in an individual with inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis (UC). In addition, the present invention provides methods for monitoring the progression of mucosal healing in an individual with a disease such as IBD. Information on mucosal healing status derived from the use of the present invention can also aid in optimizing therapy and/or monitoring the therapeutic efficiency of an anti-TNFα inhibitor drug.