Thiol self-assembled monolayers (SAMs) on Au(III) are ubioquitous systems for surface functionalization. While these systems have been studied extensively in the past there are a still points that need further investigation both from a point of view. For instance, SAMs of long chain thiols which are solid at room temperature have only been grown in solution due to their low vapor pressure. Hence, almost all the reported properties of these SAMs, such as growth mechanism, kinetics, and film structures, are based on solution-grown films. Here long chain thiol SAMs were grown in vacuum by using supersonic molecular beam (SMBD) deposition. This technique not only allows low vapor pressure thiol to be deposited in vacuum in a very controlled way, but it also enables control over the kinetic energies of the deposited molecules. Here we report a helium diffraction study of low coverage striped phase of mercaptoundecanol (MUD) and octadecanethiol (ODT) SAMs on the Au(111) surface. MUD SAMs were observed to form a (11.8 x root 3) unit cell whereas ODT SAMs adopt a (18 x root 3) unit cell. Both of the studied molecules were shown to form disordered physisorbed layers on the chemisorbed first layer, with desorption energies of 72 and 86 kJ/mol, respectively. While four desorption states could be identified for MUD with energies of 118, 136, 141, and 150 kJ/mol, ODT has one chemisorbed and one physisorbed state with desorption energies of 135 and 154 kJ/mol. The results reported here may serve as a reference for comparison of properties of solution-grown and vacuum-deposited thiol SAMs. In addition, the control over the kinetic energy may open up new possibilities in terms of applications that utilize patterned films.