A better understanding of the interactions between metal electrodes and organic molecules still represents one of the key problems in molecular electronics that needs be solved in order to optimize electron transport through a molecular device. In this contribution, the impact of widely used "alligator clips" (Au−thiol, Pd−pyridine) onto the electronic structure of the respective electrodes in metal− molecule−metal junctions has been studied using photoelectron spectroscopic tools. Different electronic properties are observed for molecules with different lengths but identical terminal groups, thereby elucidating a new aspect in the complex behavior of metal/molecule contacts.