The complex behavior of the simplest atomic-scale conductors indicates that the electrode structure itself is significant in the design of future nanoscale devices. In this study, the structural asymmetry of metallic atomic contacts formed between two macroscopic Au electrodes at room temperature was investigated. Characteristic signatures of the structural asymmetries were detected by fast current-voltage (I-V) measurements with a time resolution of approximately 100 μs. Statistical analysis of more than 300,000 I-V curves obtained from more than 1000 contact-stretching processes demonstrates that the current rectification properties are correlated with the conductance of the nanocontacts. A substantial suppression of the variation in current rectification was observed for the atomic contacts with integer multiples of the conductance quantum. Statistical analysis of the time-resolved I-V curves revealed that the current rectification variations increased significantly from 500 μs onward before the breakage of the atomic contacts. Ab initio atomistic simulations of the stretching processes and corresponding I-V characteristics confirmed the magnitude of the rectification and related it to the structural asymmetries in the breakdown process of the junctions. Overall, we provide a better understanding of the interplay between geometric and electronic structures at atomically defined metal-metal interfaces by probing charge transport properties in extremely sensitive nanocontacts.