Abundant experimental and clinical data incriminate microbial factors in the pathogenesis of inflammatory bowel diseases. Commensal bacteria, and their products, provide the constant antigenic stimulus to disequilibrate the mucosal immune system towards an overly aggressive response in a genetically susceptible host with reduced tolerance towards the autologous flora. Not all bacteria have equal proinflammatory capabilities. Some may be even beneficial as demonstrated by the anti-inflammatory effects of so-called probiotics. Further investigations are needed to translate the clear experimental and clinical evidence into benefit for the patients.