A gas chromatographic method for the determination of 1- and 3-methylhistidine in biological fluids was developed. The amino acid fraction containing 1- and 3-methylhistidine was isolated using ion-exchange chromatography. The amino acids were derivatized to N-trifluoroacetyl-O-isobutyl esters and analysed by gas chromatography with micropacked or capillary columns and an ionization-resonance detector. The conditions for the acylation of the histidines were studied and analyses of various derivatives such as N-trifluoroacetates, N-pentafluoropropionates and N-heptafluorobutyrates were tested. The detection limit of 1- and 3-methylhistidine was 50 ng per sample.