N,O-bis(trimethylsily)trifluoroacetamide (BSTFA) and N-methyl-N(trimethylsily) trifluoroacetamide (MSTFA) are common derivatization reagents used in the GC-MS analysis of estrogen steroids such as estrone (El) and 17alpha-ethinylestradiol (EE2). In this study, three trimethylsilyl (TMS) steroid derivatives, mono- and di-trimethylsilyl EE2 and mono-trimethylsilyl E1, were observed during the derivatization of EE2 with BSTFA or MSTFA and/or GC separation. Factors influencing the production of multiple TMS derivatives and their relative abundance were examined. It was found that both methanol and bisphenol A competed with estrogenic esteroids when reacting with silylation reagents, and thus affected the formation of TMS derivatives and their relative abundance in the derivatization products. Methanol was found to be more reactive than bisphenol A with the BSTFA reagent. None of the three solvents tested in this study could prevent the generation of multiple TMS derivatives during the derivatization of EE2 with BSTFA, followed by GC analysis. A similar result was observed using MSTFA as the derivative reagent followed by GC analysis. Thus, the suitability of BSTFA or MSTFA as the derivatization reagent for the determination of E1 and EE2 by GC-MS, under the conditions reported here, is questionable. This problem can be solved by adding trimethylsilylimidaz (TMSI) in the BSTFA reagent as recommended, and the performance of the method has been proved in this study.