Auto-immune disease including inflammatory bowel disease, lupus, rheumatoid arthritis, but not including hypothyroidism or psoriasis if condition has been stable for months or greater History of auto-immune disease (e.g., thyroiditis, lupus), except vitiligo No active auto-immune disease and not on therapy for auto-immune disease. Patients with a history of autoimmune-related hypothyroidism on a stable dose of thyroid replacement hormone are eligible. Patients who have adrenal insufficiency and hypophysitis from prior immunotherapy if they are on stable medical replacement doses are eligible Life expectancy of > months (exclusive of the disease for which the auto HSCT is being performed) Active auto-immune disease including connective tissue disease, uveitis, sarcoidosis, inflammatory bowel disease, or multiple sclerosis, or have a history of severe (as judged by the principal investigator) autoimmune disease requiring prolonged immunosuppressive therapy Have active auto-immune disease, including connective tissue disease, uveitis, sarcoidosis, inflammatory bowel disease, or multiple sclerosis, or have a history of severe (as judged by the principal investigator) autoimmune disease requiring prolonged immunosuppressive therapy The subject has a history of, or is reasonably suspected to meet criteria for the diagnosis of a systemic auto-immune/inflammatory disease or other autoimmune disorder with the exception of:\r\n* Vitiligo Patients with auto-immune disease, with the exception of type I diabetes or treated hypothyroidism. Significant auto-immune disease requiring hospitalization within the past two years or any history of life-threatening auto-immune disease Subjects must not have active auto-immune disease, including connective tissue disease, uveitis, sarcoidosis, inflammatory bowel disease, or multiple sclerosis, or have a history of severe (as judged by the principal investigator) autoimmune disease requiring prolonged immunosuppressive therapy PHASE I STUDY ELIGIBILITY CRITERIA:\r\nHistory of auto-immune disease requiring steroid maintenance, or history of primary immunodeficiency Prior auto-immune disease Active autoimmune or auto-inflammatory ocular disease within months History of auto-immune disease per physician discretion The subject has a history of, or is reasonably suspected to meet criteria for the diagnosis of a systemic auto-immune/inflammatory disease or other autoimmune disorder with the exception of: vitiligo, diabetes or thyroid dysfunction Patients with active auto-immune disease requiring immunosuppressive medication Auto-immune hemolytic anemia Ongoing clinically significant anemia due to factors such as iron, vitamin B, or folate deficiencies, auto-immune or hereditary hemolysis, or gastrointestinal bleeding. Patients with active neurological auto immune or inflammatory disorders(e.g. Guillain Barre Syndrome, Amyptrophic Lateral Sclerosis) History of auto-immune disease Patients with known auto-immune disease Subject who has active auto-immune disease. Active auto-immune disease Auto-immune disease Decompensated liver disease (Child-Pugh score > ) or active or past auto-immune hepatitis Active known auto-immune disease with the exception of autoimmune thyroiditis, vitiligo, and alopecia; Patients with history of autoimmune disease (excluding thyroiditis on chronic thyroid replacement therapy) or active auto-immune disease, due to a risk of exacerbation of autoimmunity with r-hIL; patients with a history of B cell malignancy due to a risk for growth with rhIL therapy Subject has significant auto-immune disease Subjects with active auto immune disorders/processes or active neurological or inflammatory disorders Significant auto-immune disease requiring hospitalization within the past two years or any history of life-threatening auto-immune disease Auto-immune disease, which: