Galaxy clusters represent the largest known population of gravitationally bound objects formed in the Universe. Cool cores are often located at the center of galaxy clusters. They are in the form of the dense, relatively cool, metal enriched intracluster medium (ICM). The presence of cool cores poses a challenge for our understanding of the thermal evolution of the ICM. SInce the ICM is losing their energy by X-ray radiation, it was expected that runaway cooling takes place and a massive starburst is induced by a cooled ICM. However, X-ray observations indicate that there is no evidence of runaway cooling and the ICM is heated. Feedback of active galactic nuclei (AGN) is considered as a plausible heating source, whereas a cluster merger is also thought as an alternative heating source. Recently, we present that gas density perturbations in cool cores are found in the residual images of the X-ray surface brightness profile after subtracting their mean profiles. We found that the thermodynamic properties of the ICM in perturbed regions indicate that the ICM is in pressure equilibrium and their gas motion is subsonic. These results are consistent with a scenario that a dominant component of gas density perturbations is generated by a cluster merger. In this talk, I will introduce our recent study of gas density perturbations in the cool cores in two representative cluster samples (i.e., CLASH and HIFLUGCS).