Inclusion Criteria: (Part A \& B) * Male X-CGD patients \> 23 months of age * Molecular diagnosis confirmed by DNA sequencing and supported by laboratory evidence for absent or reduction \> 95% of the biochemical activity of the NADPH-oxidase * At least one prior, ongoing or refractory severe infection and/or inflammatory complications requiring hospitalization despite conventional therapy * No 10/10 HLA-matched donor available after initial search of NMDP registries * No co-infection with Human Immunodeficiency Virus (HIV)-1 or -2, hepatitis B virus or hepatitis C virus, adenovirus, parvovirus B 19 or toxoplasmosis, or active infection with CMV * Written informed consent for adult patient, and assent for pediatric subjects seven years or older. * Parental/guardian and, where appropriate, child's signed consent/assent Exclusion Criteria: * Age \< 23 months * 10/10 HLA identical (A,B,C,DR,DQ) family or unrelated or cord blood donor unless there is deemed to be an unacceptable risk associated with an allogeneic procedure * Contraindication for leukapheresis or bone marrow harvest (anemia Hb \<8g/dl, cardiovascular instability, severe coagulopathy) * Appropriate organ function as outlined below must be observed within 8 weeks of entering this trial. 1. Hematologic 1. Anemia (hemoglobin \< 8 g/dL). 2. Neutropenia (absolute granulocyte count \<1,000/mm3) 3. Thrombocytopenia (platelet count \< 150,000/mm3). 4. PT or PTT \> 2X the upper limits of normal (patients with a correctable deficiency controlled on medication will not be excluded). 5. Cytogenetic abnormalities known to be associated with hematopoietic defect on peripheral blood or bone marrow. 2. Infectious a. Evidence of co-infection with HIV-1, HIV-2, hepatitis B, Hepatitis C, adenovirus, parvovirus B19, toxoplasmosis. CMV infection is allowable as long as the infection is under control. 3. Pulmonary a. Resting O2 saturation by pulse oximetry \< 90% on room air. 4. Cardiac 1. Abnormal electrocardiogram (EKG) indicating cardiac pathology. 2. Uncorrected congenital cardiac malformation with clinical symptomatology. 3. Active cardiac disease, including clinical evidence of congestive heart failure, cyanosis, hypotension. 4. Poor cardiac function as evidenced by LV ejection fraction \< 40% on echocardiogram. 5. Neurologic 1. Significant neurologic abnormality by examination. 2. Uncontrolled seizure disorder. 6. Renal 1. Renal insufficiency: serum creatinine ≥ 1.5 mg/dl, or ≥ 3+ proteinuria. 2. Abnormal serum sodium, potassium, calcium, magnesium, phosphate at grade III or IV by the Common Terminology Criteria for Adverse Events (CTCAE) version 4.0. 7. Hepatic/GI: 1. Serum transaminases \> 5X the upper limit of normal (ULN). 2. Serum bilirubin \> 2X ULN. 3. Serum glucose \> 1.5x ULN. 8. Oncologic a. Evidence of active malignant disease 9. General 1. Expected survival \< 6 months 2. Major congenital anomaly 3. Ineligible for autologous HSCT by the criteria at the clinical site. 4. Contraindication for administration of conditioning medication. (Known sensitivity to Busulfan) 5. Administration of gamma-interferon within 30 days before the infusion of transduced, autologous CD34+ cells. 6. Participation in another experimental therapeutic protocol within 6 months prior to baseline and during the study period. 7. Tested positive (definitive) for the presence of multiple types (2 or more) of anti-platelet antibodies. 8. Any other condition that, in the opinion of the Investigator, may compromise the safety or compliance of the patient or would preclude the patient from successful study completion. 9. Patient/Parent/Guardian unable or unwilling to comply with the protocol requirements. Part B Additional exclusion criteria: * Patients \>12 years of age at enrolment * Patients ≤12 years of age with a body weight \>40kg at enrolment