During recent years, molecular techniques have significantly impacted our understanding and therapeutic concepts in gastrointestinal and liver disease. In a number of diseases, diagnostic work-up includes molecular data that supplements the phenotypical evaluation. This includes monogenic diseases as well as the identification of genetic risk factors (e. g. NOD2/CARD15 mutation in Crohn's disease) and viral disease. Attempts to replace liver transplantation in hereditary liver disease by targeted molecular interventions (e. g. via viral vectors) are still experimental, but the associated techniques have improved considerably. The molecular identification of therapeutic targets was followed by the development of specifically tailored therapeutics. These agents are mainly used in the treatment of chronic inflammatory bowel disease and gastrointestinal tumors.