Gas chromatography-mass spectrometry (GC-MS) is a highly reproducible and sensitive analytical technique that has had significant use in the area of metabolite profiling. GC-MS is able to detect a wide variety of metabolites, with highly differing chemistries. In general, extracted biological samples are volatilized prior to separation on a capillary column with a stationary phase suited to the analysis of the compounds of interest. Separated compounds are eluted into a mass spectrometer equipped with an electron impact ionization source, thereby generating a quantifiable mass spectral fingerprint. This chapter describes a method for the trimethylsilyl derivatization of polar metabolites, followed by detection and relative quantification using a gas chromatograph coupled to a single quadrupole mass spectrometer. Using this method will enable the profiling of the greatest range of polar metabolites.