OBJECTIVE: There is increasing knowledge of the pathophysiology behind inflammatory bowel disease (IBD) although the exact mechanism is far from fully understood. In the era of new technology, over the last years molecular approaches have shed light on the inflammatory mechanisms and their metabolic end products. This opens for a molecular fingerprinting that can be used in the biomarker field of IBD. There is a great need of biomarkers for prediction of clinical outcome and prognostic biomarker for prediction of therapeutic effects in IBD. Although the biomarker concept is old, so far very few really useful biomarkers exist in IBD. MATERIAL AND METHODS: Here, we review the predictive and prognostic biomarkers in IBD in the era of new technologies with emphasis on the potential of molecular fingerprinting. RESULTS: Very few candidate biomarkers have been documented. The most promising candidate predictor is tumor necrosis factor-α, but there is a lack of validation. CONCLUSION: So far, there are few biomarkers documented in IBD, but we are at the start of a new scientific field that will be of great value for the handling of the disease.