Differences in the physical properties of individual cells cannot be evaluated with conventional experimental methods that are used to study groups of cells obtained from pure cultures. To examine the differences in the thermal tolerance of individual cells that are genetically identical, a method is needed to measure the thermal energy required to kill single cells. We developed a scanning thermal microscopy（SThM）system and measured the thermal conductivity of various bacterial cells, for example, spore formeing Bacillus genus and non spore-forming bacteria such as Escherichia coli. The thermal conductivity of vegetative cells（0.61 to 0.75 W/m・K）was found to be higher than that of spores（0.29 to 0.45 W/m・K）. Furthermore the newly developed method enables us to estimate the thermal energy needed to kill individual cells or spores. We believe that this method can estimate the thermal energy required to achieve the cell for sterilization by heating.