Although the tunneling rates decrease exponentially with a decay coefficient β close to 1.0 nC–1 across n-alkanethiolate (SCn) monolayer based tunneling junctions determined over a multitude of test beds, the origins of the large spread of injection current densities—the hypothetical current density, J0 (in A/cm2), that flows across the junction when n = 0—of up to 12 orders of magnitude are unclear. Every type of junction contains a certain distribution of defects induced by, for example, defects in the electrode materials or impurities. This paper describes that the presence of defects in the junctions is one of the key factors that cause an increase in the observed values of J0. We controlled the number of defects in AgTS-SCn//GaOx/EGaIn junctions by varying the geometrical contact area (Ageo) of the junction. The value of J0 (∼102 A/cm2) is independent of the junction size when Ageo is small (<9.6 × 102 μm2) but increased by 3 orders of magnitude (from 102 to 105 A/cm2) when Ageo increased from 9.6 × 102 to 1.8 × 104 μm2. With increasing J0 values the yields in nonshorting junctions decreased (from 78 to 44%) and β increased (from 1.0 to 1.2 nC–1). We show that the quality of the junctions can be qualitatively determined by examining the curvature of the dJ/dV curves (defects change the sign of the curvature from positive—associated with tunneling—to negative—associated with Joule heating) and fitting the J(V) curves to the full Simmons equation to (crudely) estimate the effective separation of the top- and bottom-electrode deff. This analysis confirmed that the electrical characteristics of large junctions are dominated by thin-area defects, while small junctions are dominated by the molecular structure.