A capillary gas chromatographic method with mass spectrometric detection for the determination of pipecolic acid in urine and plasma (or serum) has been developed. Using a quantification based on stable isotope dilution mass fragmentography the concentration of pipecolic acid was determined in urines of 34 healthy children and 8 patients with Zellweger's syndrome. The urinary pipecolic acid excretion of healthy infants decreases with age. Its concentration in urines of patients with Zellweger's syndrome was not consistently elevated. Normal values for pipecolic acid in plasma were established for 19 healthy children. Pipecolic acid concentrations in 47 urine samples (range 0.02-228.3 mmol/mol of creatinine) and 6 serum samples of Zellweger patients after oral loading with DL-pipecolic acid (range 65-1334 mumol/l) were found to correlate satisfactorily with the results obtained by an amino acid analyzer method. The major advantage of the presented method over the amino acid analyzer method concerns its greater sensitivity and its much shorter analysis time.