Crohn's disease (CD) is a chronic illness, immunologically mediated, probably induced by the exposure of the intestine to an antigen or antigens similar to the intestine, to which immunologic tolerance is lost or a dysregulated immunity ensues. The disease has a variable course, from a mild, intermittently active illness requiring only symptomatic therapy to a fulminant illness requiring potentially dangerous immunosuppressive therapy, surgery or both. The molecular defect causing CD has not been characterized, but probably involves aberrant T cell function. Although CD often responds to immunosuppressive medication including corticosteroids, azathioprine and 6-mercaptopurine, to anti inflammatory drugs such as 5 aminosalicylate (5 ASA), or to some antimicrobial agents, including metronidazole, no therapy has been curative. In patients with severe CD, who have been unresponsive to corticosteroids, azathioprine, 5 ASA, metronidazole, and infliximab, we propose to compare the efficacy of Crohn's disease non-myeloablative autologous hematopoietic stem cell transplantation (CDNST) to standard therapy. Subsequent disease activity will be followed by (1) Crohn's disease activity index (CDAI), (2) a more global severity index, the Crohn's Severity Index, (3) type and amount of therapy for CD, and (4) clinical, hematologic and biochemical studies.