Quantitative analysis of the following peroxisomal metabolites is reported: very long-chain fatty acids (VLCFA), pipecolic acid, bile acid intermediates, phytanic and pristanic acid, in plasma, urine, cerebrospinal fluid (CSF), blood spots collected at neonatal screening and amniotic fluid. An overview is given of the concentrations of these metabolites in body fluids from control subjects and all patients investigated so far in this laboratory. The method of choice is gas chromatography -- mass spectrometry (GC-MS) with electron capture detection, combined with the use of stable-isotope-labelled internal standards.