Metabolomics is a collection of powerful tools for the analysis of phenotype, both by hypothesis generation and by hypothesis testing. Building on the strengths of the “omics technologies that came before, metabolomics uniquely comprises analytical technologies that can provide diagnostic patterns via fingerprinting, absolute quantitation of targeted metabolites via pool analysis, relative quantitation of large portions of the metabolome using metabolite profiling, and tracing of the biochemical fate of individual metabolites through a metabolic system via flux analysis. Each of these technologies is supported by the two most commonly used and powerful techniques currently available for metabolomics: mass spectrometry and NMR. Mass spectrometry-based metabolomics techniques are the most sensitive for simultaneous analysis of a large number of compounds. While limited in quantitation capabilities without appropriate labeled standards, the sheer quantity of information available in a single LC-MS or GC-MS experiment can provide detailed information on the patterns of metabolite change in an entire metabolic network. NMR metabolomics complements mass spectrometry. It is limited in terms of sensitivity, but is uniquely capable of elucidating molecular structure. An important additional feature of NMR is that it is quantitative, capable of providing absolute levels of detected compounds when appropriate techniques are used.