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A dipole-layer approach is adapted to describe the electrostatic potential and electronic transport through metal/semiconductor junctions with a discontinuous monolayer of polar molecules at the metal/semiconductor interface. The effective barrier height of those junctions, which have small pinholes, embedded in a molecular layer, which introduces a negative {positive} dipole (i.e., a dipole whose negative {positive} pole is the one that is closest to the semiconductor surface) on an n-type {p-type} semiconductor, is often “tunable” by the magnitude and density of the dipoles. If the lateral dimensions of a molecule-free pinhole at the interface exceed the semiconductor depletion width, carrier transport is not influenced by the molecular layer and the “effective” barrier height is the nominal metal/semiconductor barrier height. If the molecular layer introduces a positive {negative} dipole on an n-type {p-type} semiconductor, enhanced field emission at edges of small pinholes might lead to a leakage- and/or an edge-current component resulting in an effective barrier height lower than the nominal one. We support these conclusions by direct measurements of the nm-scale electronic behaviour of a Au/n-GaAs diode with a discontinuous monolayer of dicarboxylic acids at the interface, using Ballistic Electron Emission Microscopy (BEEM). (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)