Both autologous and allogeneic haemopoietic stem cell transplantation (HSCT) have been tried in Crohn's disease (CD). In allogeneic HSCT, the host bone marrow is ablated and replaced by bone marrow from a donor. This substitution of a genetically different bone marrow is effective in a number of conditions including those with an immunological basis such as CD. While the toxicity of allogeneic HSCT has precluded its uptake in idiopathic CD, there is interest in its utility in the management of early onset infantile (inflammatory bowel disease), which behaves as a monogenic disorder, with abnormalities of the interleukin 10 signalling system as the best recognized. In autologous HSCT, the patient's own stem cells are harvested before proceeding to lymphoablation and transplantation of the patient's own uncommitted stem cells, which generate an immune system with an altered T-cell repertoire. In a limited number of cases, this has led to substantial and prolonged remission tantamount to possible cure of CD. However, case series and controlled data from the Autologous Stem Cell International Crohn's Disease study suggest that although this method has its own advantages, most patients are still at risk of redeveloping CD, albeit with an arguably improved response to conventional treatment. The availability of new treatments for CD means that an HSCT is not a suitable treatment method for a majority of patients because of its greater toxicity, even though efficacy may be superior. Wider usage would depend upon the development of protocols that are safer and better targeted.

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