Diagnostic and pathogenetic investigations of peroxisomal disorders should include the study of the macroscopic and microscopic pathology of the liver, in addition to careful clinical observations, skeletal X-ray and brain CT scan, assays of very long-chain fatty acids and bile acid intermediates, and selected enzyme activities. This review of the literature also contains novel observations about the following syndromes: cerebro-hepato-renal (Zellweger) syndrome, X-linked and neonatal adrenoleukodystrophies (ALD, NALD), NALD-like syndromes, infantile phytanic acid storage, classical Refsum disease, rhizomelic and other forms of chondrodysplasia punctata (XD, XR, AR), hyperpipecolic acidaemia, primary hyperoxaluria I, pseudo-Zellweger and Zellweger-like syndromes, and single enzyme deficiencies. Microscopic data include catalase staining and morphometry of peroxisomes, immunolocalization of beta-oxidation enzymes, detection of trilamellar, polarizing inclusions in PAS-positive macrophages, fibrosis and iron storage. Peroxisomal enlargement appears to be related to functional deficit in beta-oxidation disorders as well as in rhizomelic chondrodysplasia punctata. Because normal peroxisomal localization of active beta-oxidation enzymes can accompany a C26 beta-oxidation deficit, other mechanisms such as impaired transport of metabolites should be investigated. 'Ghost'-like organelles are shown in the liver of an infantile Refsum patient and in an NALD-like case; immuno-gold labelling of membrane proteins did not reveal ghosts in Zellweger livers.