This paper presents briefly the basic principles of operation for the mass spectrometer (MS) and gas chromatography-mass spectromtery (GCMS) systems as well as discuss some of the analytical and assay methods for indole compounds which utilize GCMS. Using 5-methoxytryptophol as an example, the development of such an assay method is examined in detail. Finally, some of the most recent methodological and instrumental developments in mass spectrometry, including field disorption mass spectrometry (FDMS), negative ion chemical ionization mass spectrometry, and isotope dilution techniques are discussed in view of the contributions they may be expected to make to the study of pineal chemistry.