Here, we present the program QContacts, which implements Voronoi polyhedra to determine atomic and residue contacts across the interface of a protein-protein interaction. While QContacts also describes hydrogen bonds, ionic pair and salt bridge interactions, we focus on QContacts’ identification of atomic contacts in a protein interface compared against the current methods. Initially, we investigated in detail the differences between QContacts, radial cutoff and Change in Solvent Accessible Surface Area (delta-SASA) methods in identifying pair-wise contacts across the binding interface. The results were assessed based on a set of 71 double cycle mutants. QContacts excelled at identifying knob-in-hole contacts. QContacts, closest atom radial cutoff and the delta-SASA methods performed well at picking out direct contacts; however, QContacts was the most accurate in excluding false positives. The significance of the differences identified between QContacts and previous methods was assessed using pair-wise contact frequencies in a broader set of 592 protein interfaces. The inaccuracies introduced by commonly used radial cutoff methods were found to produce misleading bias in the residue frequencies. This bias could compromise pair-wise potentials that are based on such frequencies. Here we show that QContacts provides a more accurate description of protein interfaces at atomic resolution than other currently available methods. QContacts is available in a web-based form at http://tsailab.tamu.edu/qcons (Fischer et al., 2006).