The metabolome is the set of small molecular mass compounds found in biological media, and metabolomics, which refers to as the analysis of metabolome in a given biological condition, deals with the large scale detection and quantification of metabolites in biological media. The metabolome is characterized by a large number of molecules exhibiting a high diversity of chemical structures and abundances, requiring complementary analytical platforms for extensive coverage. Among them, atmospheric pressure ionization Fourier transform mass spectrometry (FT/MS) instruments are now very popular because they provide accurate mass measurements with ppm and even sub-ppm errors, high and ultra-high resolving power, and also the possibility to perform MSn experiments for annotation and identification of metabolites. This chapter deals with the improvements provided by the different kinds of FT/MS instruments for metabolomics, together with their ability to cover the various analytical needs for metabolomics, from global metabolite profiling to structural characterization of compounds. The specificities of FT/MS in terms of data pre-processing and the input of accurate mass measurements for biological interpretation are also addressed.