Internal structures of surface blisters and their precursors in Si formed by H þ , D þ and He þ irradiation were examined by cross-sectional transmission electron microscopy (XTEM). The skin structures of H þ -D þ -and He þ -blisters reflected the difference in the damage accumulation, and chemical interaction between the implant ion and silicon. These differences had a direct influence on the defect structures of the damaged layer, which played essential roles in the blistering mechanisms. It was found that blister skin thickness derived by grazing incidence electron microscopy (GIEM) and electron energy-loss spectroscopy (EELS) was underestimated compared to direct measurement by XTEM. The origin of this discrepancy is discussed.