Metabolomics concerns with the comprehensive analysis of low-molecular weight metabolites occurring in metabolic pathways in biological fluids.It is a multi-disciplinary science that includes aspects of biology, chemistry, and mathematics.Information about metabolite profiles of biological fluids is important for understanding physiological states.It requires the optimal uses of sample preparation techniques and of analytical techniques such as chromatography and mass spectrometry, coupled with multivariate data analysis methods.With increasing needs of metabolomic investigations in biomedical research fields, we developed and validated achiral and chiral separation methods of amino acids, organic acids and catecholamines by gas chromatography and gas chromatography-mass spectrometry combined with graphic pattern recognition.Their applications to diverse clinical samples from patients with inherited metabolic disorders, Alzheimers disease and cancer will be presented for the monitoring of disease states and correct diagnosis.