Living cells possess the ability to tune their response to various intra- and extracellular cues, e.g., oxidative stress, nutritional deprivation, etc., which in turn leads to an assortment of different metabolites in the cellular soup. Metabolomics – the science that deals with understanding the metabolic profile of a biological system under a set of conditions – is becoming a powerful tool that helps to comprehend the mechanistic information about cellular events. The information about the small molecules present in the biological soup is now being used in different facets of research in life sciences, including natural product identification; studying pharmacological responses of potential drugs; understanding the chemical diversity of a plant/microbial species based on geographical origin; translational metabolomics of bio-fluids to understand various diseases, and cellular pathway analysis; etc. The technological challenge in the identification as well as characterization of these small molecules has been answered in part by recent advances in the field of Mass spectrometry and NMR, coupled with high-throughput separation techniques. In this chapter, we will discuss the diversity of the metabolome; primary and secondary metabolites; overview of available techniques for metabolite identification and characterization; recent advances in NMR making it amenable for the study of metabolites; and the methods used for NMR data measurement and analysis.