This is a Phase I/II clinical trial to determine the efficacy and safety of a method of ex vivo gene therapy to treat both X-linked gp91phox deficient Chronic Granulomatous Disease (CGD) and autosomal recessive p47phox deficient CGD. CGD is an inherited immune deficiency in which blood neutrophils and monocytes fail to produce superoxide and other antimicrobial oxidants, and patients get recurrent life-threatening infections. 30 CGD patients of either sex at least 5 years of age may be enrolled in addition to the 5 patients enrolled in the first phase of this trial. Patients less than 16 years of age must have an active infection or a recent relapse of infection at the time of enrollment. Patients may receive up to 6 cycles of stem cell mobilization for gene therapy at intervals of 4 weeks or longer. For up to first 3 cycles, a cycle of stem cell mobilization for gene therapy will begin with 8 daily subcutaneous injections of the combination of flt3-ligand (flt3L) at 50 micro g/kg/day plus granulocyte-macrophage colony stimulating factor (GM-CSF) at 5 micro g/kg/day for mobilization of CD34+ cells. For 3 or more of the cycles of mobilization of CD34+ cells for gene therapy (up to the maximum of 6 cycles total), the mobilization will begin with 6 daily injections of granulocyte colony stimulating factor (G-CSF) at 10 micro g/kg/day. On the last two or three days of marrow growth factor administration for mobilization of CD34+ cells, the patients will have an apheresis procedure to harvest blood mononuclear cells, thus completing a cycle of mobilization and stem cell harvest. CD34+ progenitors will be selected from the apheresis collection using the Isolex(Registered Trademark) 300i anti-CD34 monoclonal antibody/magnetic bead selection system. The purified CD34+ cells may either be placed directly into culture or may be cryopreserved as per standard blood bank procedure (freezing in autologous serum with 10% dimethylsufoxide {DMSO}) and stored frozen at liquid nitrogen temperature until thawed for ex vivo culture and transduction. For a specific gene therapy treatment of intravenously infused, gene corrected stem cells, the purified CD34+ stem cells collected, purified and frozen from one or more cycles of mobilization will be thawed and then pooled at the time of placement into culture for transduction with the virus vector. CD34+ cells will be cultured in PL2417 gas permeable plastic containers that have been pre-coated with fibronectin fragment CH-296. The growth medium will be serum-free X-VIVO 10(Registered Trademark) supplemented with 1% human serum albumin, 100 ng/ml flt3-ligand, 50 ng/ml PIXY321 and 50 ng/ml stem cell factor (SCF). Cultured CD34+ progenitors will be transduced on each of 3 or 4 days with either MFGS-p47phox or MFGS-gp91phox retrovirus vectors. The retrovirus vectors are replication defective packaged in amphotropic envelope lines engineered with the CRIP packaging elements (5' LTR-gag-pol-3'SV40polyA; 5'LTR-AMenv-3'SV40polyA). MFGS-p47phox is packaged in the murine psi-crip line, while MFGS-gp91phox is packaged in the human 293-SPA line. The clinical retrovirus vector supernate will be animal protein-free and serum free. Safety testing for endotoxin, sterility, and absence of replication competent retrovirus will be performed on the retrovirus producer lines, virus particle lots, and transduced cells. Transduced CD34+ cells will be infused into the CGD patient. Thus, there will be a total of up to six cycles of stem cell mobilization, but because the CD34+ cells from one or more cycles of mobilization may be cryopreserved and then later pooled for culture to produce a single gene corrected stem cell product for infusion, there may be fewer than six rounds (and possibly only one round) of gene therapy treatments for a patient who participates in this study. Blood will be tested periodically for the appearance and persistence of neutrophils that are functionally corrected by the gene therapy. The efficacy goal for this study is to allow CGD patients to produce autologous gene-corrected functionally normal NADPH oxidase positive neutrophils to a level of at least 1 in 1000 circulating neutrophils for at least four weeks. This may provide clinical benefit in the form of increased host defense against an ongoing or potential infection. The clinical status of patients will be monitored for any evidence of toxicity. Information obtained from this study will provide information important for achieving the ultimate goal of the development of gene therapy for CGD that will be a permanent cure for this disorder.