Until now neurotrophins like nerve growth factor (NGF), brain-derived neurotrophic factor (BDNA), neurotrophin (NT)-3 and neurotrophic factors like glial-derived neurotrophic factor (GDNF) have been almost exclusively investigated concerning their role in differentiation, growth and survival of specific neurons in the peripheral and central nervous system. However, in the last decade several non-neuronal functions of neurotrophins and neurotrophic factors have been characterized. In the gastrointestinal tract, neurotrophins and neurotrophic factors regulate neuropeptide expression, interact with immunoregulatory cells and epithelial cells and regulate motility during inflammation. This highlights this new and complex regulatory system as important and may lead to new options in the treatment of acute and chronic inflammation of the gut.