Fatigue crack initiation is caused by cyclic slip deformation in crystalline materials. Its mechanism, however, has not been clearly elucidated yet. In the present study, the surface of S45C steel which was fatigued under push-pull loading was observed by means of AFM ad then geometric configuration developed due to fatigue was measured with a high resolution. The center average height in the surface roughness increased greatly at the early stage of fatigue process and moderately increased in the following fatigue process, which occurs mainly in ferrrite portion of ferrite/pearlite microstructure. FFT analysis was achieved to examine a characteristic of geometric configuration developed on the surface of fatigued specimen. Consequently, it was found out that the power spectrum density is much greater in the frequency range corresponding to the grain size, and increases with almost the same distribution with respect to frequency as fatigue process progresses.