The fabrication of nanoscale molecular junctions usually suffers from poorly defined metal-molecule contacts. This leads to results which vary over broad ranges even if nominally no external parameter in the systemj has been changed. Based on such experiments only statistical conclusions can be drawn. For the characterization of molecular properties in such junctions it is indispensable that the contact between metal and the molecule is reproducible at the atomic scale. Of course this requirement cannot be fulfilled by simply optimizing one of the two parts (the molecule or the metallic contact). Both constituents of the contact have to be optimized as one single composite system. It could recently be shown that junctions fabricated by shadow-maks evaporation show molecule specific behaviour. The important difference to other existing techniques is the high reproducibility of these results. We therefore plan to investigate the influence of different molecular endgroup/metal combinations on the conduction mechanism through the molecular junction systematically.