Two different procedures for the methylation of conjugated linoleic acid isomers (CLA) were compared by silver ion (Ag+)-HPLC. The base-catalysed method followed by an acid-catalysed method (NaOCH3/BF3), and base hydrolysis followed by methylation with diazomethane in diethyl ether (diazomethane) were used to prepare fatty acid methyl esters from lipids present in subcutaneous adipose tissue from beef steers. The repeatability θ of the two derivatisation methods was high (>0.9) for the major CLA isomers cis-9,trans-11 and trans-11,cis-13. A significant difference between the methods was found for the four isomers trans-11,trans-13, trans-10,trans-12, trans-9,trans-11, and trans-8,trans-10 and for the sum of total trans/trans isomers for both absolute (mg/100 g) and relative (%), which were higher with the NaOCH3/BF3 method. For the main isomer cis-9,trans-11 and the sum of total CLA isomers, a higher concentration was identified with the diazomethane method (781.2 mg/100 g vs. 749.3 mg/100 g and 991.59 vs. 962.99, respectively).