A two-step auto-injector has been developed for the automated on-column derivatization and subsequent GC-MS of amine-type drugs and metabolites. To effectively derivatize such analytes, this injector has been designed to inject the derivatization reagent several seconds after the sample has been injected. Eleven kinds of amphetamine-type stimulants (ATS) and their typical metabolites were examined, using the trifluoroacetylation reagent N-methyl bis(trifluoroacetamide) (MBTFA). Although the quantitative derivatization of the hydroxyl groups was difficult, this technique was successfully applied to the determination of ATS in urine, blood, and hair specimens. The detection limits of methamphetamine and amphetamine in hair were 0.2 and 0.1 ng/mg hair, respectively, in the full-scan mode, when a 10 mg hair sample is analyzed.