An atomically flat SrTiO3(001) surface was successfully obtained by combining ultrasonic agitation and subsequent annealing at 1000 °C in air. The topographic images taken using an atomic force microscope revealed that the surface was composed of clear atomic-steps and atomically smooth terraces. The steps were 0.2 nm in height corresponding to half of the unit cell height of SrTiO3, or the single atomic-layer height. The terraces were categorized into two types; wide and narrow terraces appear alternately. Surface composition analyzed by coaxial impact collision ion scattering spectroscopy indicated that the topmost surface was covered by domains of the SrO and TiO2 layers, where the latter domain was dominant. The result suggests that the topmost surface of the narrow terrace was terminated by SrO and the wide terrace by TiO2. This was further examined by the use of a friction force microscopy technique with which we were able to distinguish the different surface terminations.