• Treat patients with Chronic Granulomatous Disease refractory to conventional therapy and without a HLA matched sibling donor by performing stem cell transplantation from 5/6 or 6/6 HLA matched unrelated or 5/6 or 6/6 HLA phenotype matched related donors. [ Time Frame: 120 days ] [ Designated as safety issue: Yes ]
  
• Estimate engraftment rate [ Time Frame: 120 days ] [ Designated as safety issue: Yes ]
  
• To estimate the risk for acute and chronic GVHD and regimen related morbidity/mortality for patients with CGD following SCT from 5/6 or 6/6 HLA matched unrelated or 5/6 or 6/6 HLA phenotype matched related donors. [ Time Frame: 120 days ] [ Designated as safety issue: Yes ]
  
• To examine the potential for reversal of organ toxicity (e.g. lung, liver, intestine) following engraftment and stable normal neutrophil function. [ Time Frame: 120 days ] [ Designated as safety issue: No ]
  

Drug: Busulfan

days -9 through -6

1 mg/kg initially (based on weight)

Drug: alemtuzumab
day -5 through day -2 dose: based on weight
Drug: Cyclophosphamide
days -5 through -2 50 mg/kg
Drug: Fludarabine
30 mg/m^2 day -5 through day -2
Drug: cyclosporine
Therapy: Cyclosporine will be administered beginning day -2. Initial dose will 5 mg/kg infused over 24 hours.
Drug: MESNA
days -5 through -2
Procedure: stem cell infusion
Stem Cell: Either bone marrow, cord blood, or peripheral blood stem cells may be used for stem cell transplantation. It is desired to infuse: for bone marrow, nucleated cells ≥ 4 X 10^8/kg recipient weight; for cord blood ≥ 3 X 10^7/kg nucleated cells; for peripheral blood stem cells ≥ 1 X 10^/kg CD34+ cells.

Inclusion Criteria:

• CGD patients as documented by an abnormal NBT assay in a male patient and/or abnormal NADPH enzyme mutation confirmed by genetic analysis with abnormal NBT.
• Patients must not have an HLA genotype identical donor
• Patients must have a 5/6 or 6/6 HLA matched unrelated donor or a 5/6 or 6/6 HLA phenotype matched related donor.
• Patients must have had at least one serious infection characteristic of those manifested in patients with CGD.
• Patients should have an unsatisfactory response to g-interferon defined as severe invasive infection while on therapy or intolerance to interferon necessitating withdrawal from treatment.
• Patients must not have active infection. An active infection may include the following: 1) clinical findings consistent with an infection such as fever, cavitary organ lesions, osteomyelitis 2) progression of presumed infection based upon findings of diagnostic imaging [two or more studies at least 1 month a part]
• No cumulative organ dysfunction that in the estimation of the treating physicians will diminish the patient?s likelihood to survive this procedure.
• Negative pregnancy test for post-pubertal female patients.
• Echocardiogram shortening fraction >/= 28%.
• DLCO 50% predicted or FEV1 >/= 50% predicted

Exclusion Criteria:

• Markedly elevated C reactive protein or sedimentation rate relative to patient's baseline.
• Invasive bone or bone marrow disease.
• Lack of potential hematologic blood product donors in the past (related to McLeod phenotype).