We studied the influence of the end group of the alkylsilane molecule used in Self Assembled Monolayer (SAM) in Silicon/SAM/Metal junctions. By Inelastic Electron Tunneling spectroscopy (IETS), we showed the formation of a covalent bond between the molecules and the gold electrode in the case of a thiol terminated alkylsilane. By electrical characterizations, we demonstrated that the thiol group at the interface avoids diffusion of gold into the molecule even for a 3 carbons chain. For this short molecule, we observed pure tunnel conduction with barrier height at the monolayer/Si and monolayer/Au interfaces found to be respectively 2.14 and 2.56 eV. These values were obtained using Simmons equation with an effective mass parameter m * = 0.16me (me = mass of the electron).This extends the demonstration of the excellent tunnel dielectric behavior of these organic monolayers down to 3 carbon atoms with a thiol/Au bond at the interface. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)