The incidence and prevalence of inflammatory bowel disease is increasing in Western countries. Current therapies, ranging from anti-inflammatory drugs, immunosuppressive regimens to new biological therapies, remain inadequate. Advances in our understanding of the pathophysiological mechanisms underlying the pathogenetic disease process and the recent findings on the regenerative and immunoregulatory potential of stem cells open new opportunities in the therapy of inflammatory bowel disease. Therapeutic modalities, including hematopoietic stem cells, adult mesenchymal stem/stromal cells, and the recently identified amniotic origin stem cells, attracted much attention in the recent years. The current review highlights the recent pivotal findings for stem cell-based approaches to inflammatory bowel disease therapy.