In the present investigation we report selection of the N-methyl-N-(tert.-butydimethylsilyl)trifluoroacetamide (MTBSTFA) reagent as the most comprehensive derivatization protocol among 17 tested reactions covering trifluoroacetylation, pentafluorobenzylation, methylations, and trimethylsilylations. MTBSTFA allowed easy and robust tert.-butyldimethylsilyl derivatization of 1-aminocyclopropane-1-carboxylic acid, indole-3-acetic acid, (+/-)-jasmonic acid, salicylic acid, (+/-)-abscisic acid, meta-topolin, and trans-zeatin. Detection limits as analysed by selected ion monitoring quadrupole GC-MS were 0.2, 0.01, 1.0, 0.02, 0.3, 0.3, and 0.9 pmol of injected substance, respectively. Analysis of gibberellic acid A3, trans-zeatin riboside and (+/-)-abscisic acid-beta-D-glucopyranosyl ester was best when coupled by splitting extracts and trimethysilylation. The MTBSTFA derivatization protocol was optimised, and validated. The preparation was insensitive to 2% residual water and to < or = 1 day storage at room temperature. The final scheme was highly reproducible and successfully applied to extracts from approximately 300 mg (fresh mass) of tobacco (Nicotiana tabacum) root and Arabidopsis thaliana seedling.