Metabolomics is an interdisciplinary field with applications in many areas. Analytes include metabolites involved in pathways such as glycolysis, amino acid metabolism, the Krebs cycle, etc. However, the metabolites involved in these biosynthetic pathways are typically highly polar molecules, which represent a major challenge for chromatographic analysis. Whilst there have been significant efforts to address the difficulties involved in the determination of polar metabolites the comprehensive profiling of the polar metabolome remains problematic. The current review summarizes current approaches, advances and trends in the use of liquid chromatography/mass spectrometry as it attempts to address the major instrumental and intellectual challenges involved in mapping the polar metabolome.