This chapter discusses hyphenated chromatography–spectroscopy techniques and also the three areas of combined gas chromatography–mass spectrometry (GC–MS), liquid chromatography–mass spectrometry (LC–MS), and liquid chromatography–nuclear magnetic resonance spectroscopy (LC–NMR). The combination of separation techniques with spectroscopy has provided powerful tools. To fully utilize the power of combined chromatography–mass spectrometry techniques, it is necessary to understand the information and nuances provided by MS in its various forms. These novel systems have solved many of the problems associated with structure elucidation of low-level impurities. LC-NMR and its various derivatives are ideally suited for looking at simple regiochemical issues in relatively complex systems. In some cases, full structural elucidation of unknown compounds can be completed, although this will become more routine with some of the recent advances such as peak trapping in combination with cryogenic flow-probes. There are many examples of successful applications of LC–NMR and LC–NMR/MS to very complex systems. The principal advantage is that in most cases, NMR and MS data can be collected on an identical sample, thus eliminating the possibility of isolation-induced decomposition.