The widespread availability, suitability, and high sensitivity of chromatography-mass spectrometry for chemical profiling analysis of multi-component biosamples are demonstrated by the comprehensive analysis of metabolites in all kind of biofluids or tissue and cell extracts. This review provides an overview of current chromatographic-mass spectrometric metabonomic methods and applications. The focus is on the description of global metabolic profiling techniques as well as on additional important aspects of metabonomics research such as sample pretreatment and information mining methods including strategies for the identification of potential biomarkers.