Rectal mucosa biopsy specimens from five controls and three infants with Zellweger syndrome were investigated morphologically and biochemically to elucidate peroxisomal structure and functions in the human rectal mucosa and to develop a simple method for an early postnatal diagnosis of peroxisomal deficiency disorders. After the alkaline 3,3'-diaminobenzidine reaction, peroxisomes of the rectal mucosa from the controls could be identified, electron microscopically, but not light microscopically. However, they were strongly stained using an immunoenzyme technique applied to semi-thin Epon sections and then were clearly visible under the light microscope. However, no positive granules were observed in the specimens of infants with Zellweger syndrome, using either of the two staining techniques. On immunoblot analysis, immunoreactive proteins of peroxisomal acyl-CoA oxidase and 3-ketoacyl-CoA thiolase were present in rectal mucosae from the controls; however, these enzyme proteins were not detected in tissues from the patients. Activity of dihydroxyacetone phosphate acyltransferase was detectable in rectal mucosae from the controls, whereas in those from infants with Zellweger syndrome, the activity of this enzyme was greatly reduced. These observations indicate that the peroxisomal structure and multiple functions are present in the rectal mucosa and that rectal biopsy is of potential value for the early and less invasive detection of Zellweger syndrome and other peroxisomal disorders.