Four different methods for methylating conjugated linoleic acid (CLA) were compared. The HCl/MeOH and BF(3)/MeOH methods were tested under different time and temperature combinations. Increasing temperature and/or incubation time for either method decreased the cis-9,trans-11 and trans-10,cis-12 isomers, but trans-9,trans-11/trans-10,trans-12 isomers and artifacts (allylic methoxide) were increased. In addition, the triacylglyceride form of CLA was tested using the above methods and NaOMe at various temperatures for 20 min. The NaOMe did not generate methoxy artifacts. However, there were impurities in GC after methylation with NaOMe as well as with BF(3)/MeOH. The (trimethylsilyl)diazomethane method, which is a mild and easy alternative, was tested. Free forms of fatty acids were easily, but not completely, methylated by this method. Also, the method generated artifacts (trimethylsilyl CLA esters) and impurities (trimethylsilyl) that would interfere with short-chain fatty-acid analysis by GC.