Aim: To analyze surface roughness and three-dimensional (3D) scanning topography parameters of zirconia implants before and after photofunctionalization by atomic force microscopy (AFM). Materials and Methods: Ten commercially available zirconia implants five each in the study and control group were taken. The study group was subjected to ultraviolet (UV) radiation for 48 h using the shorter wavelength of 254 nm. After washing all the implants with 70% alcohol and drying, 3D surface topography and roughness parameters were analyzed using CSC 17 probe AFM at three different magnifications 25 mu m, 50 mu m, and 80 mu m, respectively. Results: The surface topography and calculated mean amplitude, spatial, and hybrid parameters of the study group were higher than the control group (P < 0.05) in all three magnifications. Up to scale depth and peak value for the study and control group were (-0.4-0.4: -2-1) (-0.75 to 0.6:-1-1.3) (-0.75--0.5: -1.5-1.3) for the study and control group at 25, 50, and 80 mu m magnification, respectively. This indicates that photofunctionalization increased surface roughness of Zirconia implants to desirable extent. Conclusion: There is a definite difference in the quantitative topographic characteristics with zirconia implants being microroughned after photofunctionalization (UV treatment).