This is a review of the clinical responses and prospectus of new therapies following use of allogeneic hematopoietic stem cell transplantation for the treatment of the following disorders: Hurlers syndrome (MPS 1-H), globoid cell leukodystrophy (GLD; Krabbes disease), adrenoleukodystrophy, metachromatic leukodystrophy, Wolmans disease, I-cell disease (mucolipidosis II; MLS-II), alpha-mannosidosis, fucosidosis, Niemann-Pick B/A disease, Slys disease (MPS VII), Gauchers disease (Gaucher-II-III), Battens disease, Farbers disease, Sanfilippo syndrome (MPS-III), Hunters disease (MPS-II), Maroteaux-Lamy syndrome (MPS-VI), and aspartylglucosaminuria (AGU). Over 500 patients with lysosomal and peroxisomal metabolic storage diseases due to deficiency of primary enzymes have been treated with hematopoietic stem cell transplantation since the initial patient was treated a quarter of century ago. Normal enzymatic activity has been robust and continuous over these years without the need for any medication. Proof of principle has been reported for multiple positive effects including that of the reconstruction of the central nervous system. Furthermore, the excellent engraftment rate along with significantly diminished graft-vs-host-disease needs to be emphasized. The genetic diseases enumerated above have remarkable differences from those discussed elsewhere in this issue of Seminars in Immunopathology. Each has a greater genetic heterogeneity. Misdiagnosis resulting in delay of treatment and further decline of function and ultimate quality of life occurs almost all the time. Neonatal screening of these diseases will be mandatory to vastly improve outcomes. Plans are being implemented to use dried blood spots on filter paper, as is commonly done for many other genetic diseases. Many new therapies are being adopted which should enhance positivity and acceptance of treatment by hematopoietic stem cell transplantation.