SummaryThis work describes methodical studies of thermally assisted hydrolysis and methylation (THM) of fatty acids (FA) and triglycerides comparing different derivatization reagents, such as tetramethylammonium hydroxide (TMAH), tetramethylammonium acetate (TMAAc), trimethylsulfonium hydroxide (TMSH), trimethylphenylamine hydroxide (TMPAH), and (m-trifluoromethylphenyl) trimethylammonium hydroxide (MethPrep 2). The performance of these reagents using different injection techniques, such as pyrolysis, hot split injection, and programmed temperature vaporization (PTV) has been investigated.Itwas found that the PTV-injection can be used for quantitative in-situ methylation of free fatly acids. THM of triglycerides in a PTV injector is less effective than THM in a pyrolyzer. The highest yields of fatly acid methyl esters (FAMEs) were obtained using TMPAH as reagent. Generally THM of unsaturated triglycerides did not result in complete trans-methylation.