In recent years, novel insights have been made into the role of bacterial microflora in health and disease. Commensal flora manipulation by probiotic bacteria has been investigated in human and experimental inflammatory bowel disease (IBD). In particular, animal models of IBD offer the opportunity to address important issues regarding indication, therapeutic efficacy and mechanism of action of the probiotic bacteria. Despite the appealing results of many published studies, fundamental questions still remain unanswered. Further studies on appropriate animal models are needed in order to better clarify our knowledge about probiotic bacteria and their potential application as a valid therapeutic option in IBD patients.