Rails are subjected to damage from rolling contact fatigue, which leads to defects such as cracks. Rolling contact fatigue damages on the surface of rail such as head check, squats are one of growing problems. Another form of rail surface damage, known as "Ballast imprint" has become apparent. This form of damage is associated with ballast particles becoming trapped between the wheel and the surface of rail. These defects are still one of the key reasons for rail maintenance and replacement. In this study, we have investigated whether the ballast imprint is an initiator of head check type cracks and effect of defect size using Finite element analysis. The FE analysis were used to investigate stresses and strains in subsurface of defects according to variation of defect size. Based on loading cycles obtained from FE analysis, fatigue analysis for each point was carried out.