We investigated intracellular localization of peroxisomal proteins in fibroblasts from patients with Zellweger syndrome and neonatal adrenoleukodystrophy in whom peroxisomes were morphologically deficient or severely decreased. Indirect immunofluorescence staining revealed that catalase was mainly detected in the cytosol of fibroblasts from these patients, but a small amount of catalase was detected in granular pattern in a small percentage of cells. Double immunofluorescence staining revealed that catalase-containing particles in these patients also contained acyl-CoA oxidase and nonspecific lipid transfer protein. However, a 70 kD integral membrane protein and 3-ketoacyl-CoA thiolase were detected in all cells in granular pattern. Subcellular fractionation using digitonin after cell labeling revealed that a small amount of acyl-CoA oxidase and about half of thiolase in the precursor form were detected in the particulate fraction. These data suggest that the mechanisms of the transport and processing of catalase, acyl-CoA oxidase and nonspecific lipid transfer protein are different from those of the 70 kD integral membrane protein and 3-ketoacyl-CoA thiolase.