A combined electronic transport-structure characterization of self-assembled monolayers (MLs) of alkyl-phosphonate (AP) chains on Al-AlOx substrates indicates a strong molecular structural effect on charge transport. On the basis of X-ray reflectivity, XPS, and FTIR data, we conclude that "long" APs (C14 and C16) form much denser MLs than do "short" APs (C8, C10, C12). While current through all junctions showed a tunneling-like exponential length-attenuation, junctions with sparsely packed "short" AP MLs attenuate the current relatively more efficiently than those with densely packed, "long" ones. Furthermore, "long" AP ML junctions showed strong bias variation of the length decay coefficient, beta, while for "short" AP ML junctions beta is nearly independent of bias. Therefore, even for these simple molecular systems made up of what are considered to be inert molecules, the tunneling distance cannot be varied independently of other electrical properties, as is commonly assumed.