SAM formation of undecanethiol (UDT) and mercaptoundecanoic acid (11-MUA) on Au(111) and on gold foils, using wet chemical preparation methods as well as physical vapor deposition (PVD) in UHV, has been studied by means of thermal desorption spectroscopy (TDS), low energy electron diffraction (LEED), and Auger electron spectroscopy (AES). The main aim of this study was to explore the possible application of TDS to characterize the quality of a SAM and to determine its thermal stability. The influence of various parameters, like substrate pretreatment, film formation method, and type of the functional end group, has been studied in detail. Three different temperature regimes can be identified in TDS, which yields specific information about the organic layer: Desorption of disulfides around 400 K can be shown to result from standing molecules in a well-defined SAM. Desorption of intact molecules and of molecules with split-off sulfur is observed around 500 K. resulting from lying molecules. Finally, desorption of an appreciable amount of gold-containing molecules is observed around 700 K. This is more pronounced for 11-MUA than for UDT, and in addition more pronounced for solution-based SAMs than for PVD prepared SAMs. These results emphasize the important role of gold adatoms in SAM formation, as recently discussed in the literature.