Metabolomics provides a powerful set of tools for pharmaceutical and clinical research in a number of important areas that include drug development, early disease detection, patient stratification for treatment, and information on disease processes. With its ability to discover new metabolic markers, metabolomics (as well as metabolic profiling and metabonomics) is highly effective for drug development by providing early preclinical indications of efficacy and toxicity. The most information-rich techniques currently employed in metabolomics-based studies today are nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS). NMR spectra of untreated biosamples provide an overview of all metabolites present, and the complete spectrum can be used as a fingerprint of metabolic status. Analysis by multivariate statistical methods is used to identify potential biomarkers of altered metabolism that can improve the understanding of the health and disease processes. Current trends and recent advances in NMR-based metabolomics are focused on the development of advanced NMR methods, improved multivariate statistical data analysis, and a number of efforts to identify altered metabolites and pathways. Applications in the areas of toxicology, inborn errors of metabolism, cardiovascular disease, and cancer detection are described, and the prospects and the future directions of the technology are highlighted.