Polyphenols are a group of plant secondary metabolites with a wide range of structural differences. In many cases, in vitro and in vivo studies of polyphenols revealed beneficial health effects. The mass spectrometric characterization of polyphenols can be the key to understanding the metabolism and resorption of this group of substances. For structure elucidation of polyphenolic compounds nuclear magnectic resonance spectroscopy is the method of choice. Due to the broad structure variability and the sometimes relatively low concentrations of polyphenols and/or their metabolites in foods as well as physiological samples, mass spectrometry could be an alternative for structure elucidation. Especially high-resolution mass spectrometry, for example, Fourier transformation mass spectrometry (FTMS), is a valuable tool. Using a FTMS system, a systematic approach to the fragmentation behavior of phenolic and polyphenolic compounds was chosen to verify the influence of the structure on the fragmentation pattern of the different substances. Depending on the structure, specific fragment ions could be detected. Therefore, it is possible to gain reliable information about the structure of the pseudomolecular ion from its fragmentation spectrum, which is of great aid in the structure elucidation of unknown polyphenols and/or their metabolites.