Peroxisomes are membrane-bound subcellular organelles that are involved in a variety of cellular functions. Disorders of peroxisomes, either in their assembly or single enzyme deficiencies, manifest themselves in the nervous system both in development and later in life. Most peroxisomal matrix proteins are targeted using one of the targeting sequences, whereas integral peroxisomal membrane proteins employ a different method. Peroxisomal importation is unique, allowing the importation of oligomerized proteins, and uses a specific extended shuttle system of receptor and cargo. The understanding of peroxisomal assembly is important because peroxisomal biogenesis disorders such as Zellweger syndrome result from these defects, and the resulting failure causes widespread deficiencies in peroxisomal biochemical function. X-linked adrenoleukodystrophy, representing the other group of peroxisomal disorders, is caused by the lack of the adrenoleukodystrophy protein, with an accumulation of very long chain fatty acids. New information on clinical incidence, phenotypic variability, and pathogenesis is becoming available and will have implications for possible therapies.