The requirement for diagnostic surgical operations of gastrointestinal system diseases significantly decreases with the help of proper diagnostic tools. These modalities are also beneficial for identifying postoperative complications, allowing us to diagnose them in earlier stages, and increasing the postoperative survival rates. Biomarkers are considered an integral part of diagnostic examinations. Developments of biomarkers used for diagnosing and treating abdominal diseases are essential for improving our capabilities in non-invasive monitoring. In this chapter, we review both the novel and the routine biomarkers in the diagnosis and follow-up of gastrointestinal system diseases.