This trial is evaluating the use of combining immunosuppression and the patient's bone marrow stem cells in patients with serious diseases of the immune system which have not responded to conventional treatments. The trial is being conducted at St Vincent's Hospital in Sydney and began recruiting patients in March 2011 with plans to recruit 30 subjects by December 2015. The conditions being investigated in the trial include Scleroderma, Multiple Sclerosis, Systemic Lupus Erythematosus (SLE), vasculitis, Crohn's disease and Behcet's disease. Participants will be given Granulocyte Colony Stimulating Factor (G-CSF) to stimulate the bone marrow into releasing stem cells, which will then be harvested from the blood of each participant. The patients will then undergo a course of intensive chemotherapy and/or immunotherapy depending on the individual condition after which they will receive an infusion of their own stem cells. Participants will be monitored for complications and assessed for changes in their clinical condition.