Biomarkers can be used almost at any time point for diagnosis and monitoring inflammatory bowel disease (IBD) patients. The readout could be from blood samples (serology, and genomic DNA), or from stool samples. The clinical implications of using biomarkers include the diagnosis of IBD, differential diagnosis between Crohn’s disease (CD) and ulcerative colitis (UC), prognosis predicting, monitoring the treatment response or accessing the mucosal healing status, and even to predict disease relapse. We will discuss the comparison between markers in order to helping minimizing the invasive procedures but improve quality of care for our IBD patients.