In metabolomics studies, optimal liquid chromatography separations prior to mass spectrometric analysis are important with regard to identification of metabolites as distinct from their isomers, and for differentiation of genuine metabolites from fragments and adducts of other molecules and from environmental and system peaks. The role of liquid chromatography in mass spectrometry based metabolomics is reviewed. The basic principles behind liquid chromatographic separations are discussed with regard to the types of interaction which can occur with stationary phases. Examples are given in order to illustrate the importance of liquid chromatography in verifying metabolite identity and also to illustrate the different types of separation produced by the various chromatographic phases available. Applications of reversed phase chromatography in metabolomics studies are reviewed for the last three years. Some examples of derivatisation, prior to liquid chromatography, which can be used in order to enhance mass spectrometric detection are covered. The review of other chromatographic methods which are less commonly used than reversed phase chromatography covers a period of six years since these methods present a wider range of stationary phase chemistries. There is a short review of lipidomics methods using liquid chromatography mass spectrometry drawn from the last two years.