Very recently, beta-keto derivatives of 3,4-methylenedioxyamphetamines (MDAs) have appeared on the illicit drug market. In the present study, we synthesized three isomers of beta-keto derivatives of MDAs, 2-methylamino-1-(3,4-methylenedioxyphenyl)butan-1-one (bk-MBDB), 2-ethylamino-1-(3,4-methylenedioxyphenyl) propan-1-one (bk-MDEA), and 2-dimethylamino-1-(3,4-methylenedioxyphenyl)propan-1-one (bk-MDDMA), and measured their electron ionization mass spectra without and with trifluoroacetyl (TFA) derivatization using gas chromatography-mass spectrometry (GC-MS). Although the spectral profiles of the three isomers were very similar to each other in both the free and TFA-derivatized forms, there were characteristic peaks at m/z 44 and 140, for bk-MDEA without and with TFA derivatization, respectively; a peak at m/z 110 for bk-MBDB-TFA was also characteristic. These peaks are useful for discrimination of an isomer from others. All isomers could be well separated in both free and TFA-derivatized forms using a slightly polar fused-silica capillary GC column DB-5MS. The present data are likely to be very useful for actual identification and quantitation of beta-keto analogues of MDAs by GC-MS, because abuse of these materials is expected to spread worldwide in the near future.