For more than 30 years, electron ionization mass spectrometry (EIMS) has played a key role in the structural determination of small biological compounds, largely because it has three advantages to offer: very high sensitivity compared to other structural methods, such as nuclear magnetic resonance and infrared spectrometry, the possibility for analysis of mixtures, and the wealth of data in the spectra that can provide information about structural details. However, the use of EIMS for the structure elucidation of larger biological molecules is limited by the necessity for vaporizing samples before ionization, a process that causes the thermal degradation of high-mol-wt and/or polar compounds. More recently, the development of “softer” methods of ionization that do not require vaporization prior to ionization has substantially overcome the problem of thermal decomposition, but these ionization methods impart little excess energy to the molecular ions and result in spectra that contain few, if any, fragment ions. In order to obtain detailed information about structure, therefore, the molecular ions must be decomposed and the mass spectra of the decomposition products recorded. For this type of analysis, a tandem mass spectrometer is employed. The resulting spectra include product (fragment) ions derived from a single precursor (parent) ion, provide structural details, such as amino acid or sugar sequence and residue modifications, and identify the components of conjugated lipids or other adducts. In the case of samples that are mixtures, the structures of each of the components can be specifically determined. A brief survey of tandem mass spectrometry as it is employed for the elucidation of several important compound types is presented here, using examples from the author’s research and collaborations. For a comprehensive review of current mass spectral approaches to the structure determination of biologically significant compounds, the reader is referred to a recent volume edited by J. A. McCloskey (1).