The aim of this study was to investigate the topography of the apical portion of 4 different commercially available standardized gutta-percha (GP) cones with atomic force microscopy (AFM). GP cones (Analytic, Dentsply, Tanari, and Endo Points) were cut 3 mm from the tip, attached in a glass base, and positioned in the AFM. Analyses were performed on 3 different regions of the GP sample and on 3 separate points of each region. Root mean square (RMS) parameters for topographic amplitudes and lateral force variations were calculated. The differences among GP brands were tested by ANOVA with a Fisher protected LSD test of multiple comparisons. According to our results, only Endo Points showed similar behavior between 2 parameters assessed (P <.05). All brands showed normally distributed deep depression in the apical portions, which are within the same scale as proteins and bacterial products that the cones should be blocking. AFM offers a powerful new tool to directly evaluate the characterization of GP cone surfaces.