It was proposed in 1974 that molecules could rectify, but molecular diodes with simultaneously high rectification ratios, yields of working junctions, and reproducibility are rare, despite a huge body of experimental work. Although every type of molecular junction contains a certain distribution of defects induced by the topography of the surface, the roles of these defects in the device performance are rarely studied. We show that control over the topography of the bottom electrode in self-assembled monolayer (SAM)-based junctions in terms of the number of grains, the width of the grain boundaries, and the roughness improves the yield of working junctions from 60% to near 100%, increases reproducibility by a factor of 3, and boosts the rectification ratio of a molecular diode (from nearly unity to ∼1.0 × 102) by minimizing the leakage currents. We found that commonly used metal surfaces fabricated by direct deposition methods are inferior to template-stripped surfaces, which are flat and contain only small areas of exposed grain boundaries, at which SAMs cannot pack well. Thus, for molecular diodes to perform well, it is crucial to minimize leakage currents by limiting the amount of exposed grain boundaries.