A fully automated identification system for 35 benzodiazepines and their 29 metabolites was developed by gas chromatography-mass spectrometry (GC-MS) with a DB-5MS fused silica capillary column after trimethylsilyl (TMS) and trifluoroacetyl (TFA) derivatization, followed by registering both their retention times and mass spectra as the standard library data. All the analytes except for rilmazafone and haloxazolam were detectable with and/or without TMS derivatization. TFA derivatization was found to be more effective in the more sensitive analysis of oxazolo-benzodiazepines except for flutazolam. Also, correction of their retention times by alkanes enabled to accurately identify on the different GC-MS systems with different lots of columns. The present system allowed us to identify benzodiazepines and their metabolites in urine and blood more readily in a much shorter time, and it will be a powerful system for the analysis of benzodiazepines in the forensic chemistry and toxicology fields.