A method for measurement of epsilon-N-trimethyllysine in human blood plasma and urine is described. An internal standard, delta-N-trimethylornithine, was added to plasma and urine specimens and the mixtures were deproteinized and/or hydrolyzed. Preliminary purification of epsilon-N-trimethyllysine and delta-N-trimethylornithine was achieved by sequential cation-exchange--anion-exchange chromatography. Amino acids in the column eluates were derivatized with o-phthalaldehyde and mercaptoethanol, and were separated by isocratic reversed-phase high-performance liquid chromatography in the presence of an ion-pairing reagent. Quantitation was achieved by post-column fluorometry. The limit of detection was 5 pmol of epsilon-N-trimethyllysine injected into the chromatograph. The procedure was suitable for determination of epsilon-N-trimethyllysine in 1 ml of plasma or 0.2-0.4 ml of urine. The method was applied to measurements of epsilon-N-trimethyllysine in plasma and urine of four systemic carnitine deficiency patients and six normal subjects. Plasma epsilon-N-trimethyllysine concentration was significantly lower in systemic carnitine deficiency patients compared to normal individuals, but no significant difference in urinary epsilon-N-trimethyllysine excretion was observed between the two groups.