Nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) are the principal methods of metabolomics, the branch of ‘-omics’ that deals with small molecules. Although MS is gaining popularity in metabolomics, NMR enjoys a number of key advantages because it is nondestructive, unbiased, quantitative, does not require separation or derivatization, and is amenable to compounds that are difficult to analyze by gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). There are two general approaches to the use of NMR for profiling studies: an untargeted approach, which uses chemometric analysis; and a targeted approach, which aims to quantify known compounds in the extract. These approaches, however, are not mutually exclusive and will likely converge in the future. This paper will describe the basic theoretical principles that should be considered to develop NMR into a standard quantitative method. Although 1H NMR is more sensitive, 13C NMR spectra are simpler with less overlapping signals and are less affected by different magnetic field strengths. Various applications of 1H and 13C NMR for the profiling of natural products are described. The use of two-dimensional 1H NMR has been used to overcome problems of spectral overlap. The standardization of the NMR protocol will make it a more useful tool for the profiling of natural products extracts.