Application tests for advanced TEM analysis techniques were carried out to study the cement alteration processes associated with water penetration at high spatial resolution. Prior to TEM analysis, we measured the changes in the penetration coefficient and determined the characteristics of the penetrating water in order to gain a fuller understanding of the overall process. These experiments revealed that the process begins with the preferential dissolution of Ca(OH) 2 . After most of the Ca(OH) 2 is dissolved out, the penetration coefficient increases, while the pH value of the water decreases. It has been demonstrated that scanning transmission electron microscope (STEM) techniques are quite useful for determining local structures and compositions in the cement at sub-micron meter spatial resolution. The preferential dissolution of Ca ions results in refinement of cement grains. When the Ca/Si ratio decreases to 1.05, most grains have a round shape in the sub-micron range. X-ray mapping suggests the formation of 3CaOÁAl 2 O 3 Á xSiO 2 Á(6À2x)H 2 O (x¼0{3). Ettringite has been mostly dissolved out. But Mg ions remain still in form of brucite. When Ca/Si reaches 0.91, the morphology has changed to a mixture of fibers and granules. The fibers have been identified as a mixture of Calcium Silicate Hydrate Gel and silica gel. Quantitative EDX composition analyses have demonstrated that the granules are altered products of hydrogrossular, 3CaOÁAl 2 O 3 Á2SiO 2 Á2H 2 O, which have been predicted by previous theoretical studies. It is also been shown that hydrotalcite with Mg and Al has been also formed. The results thus obtained are in principle in accordance with the process predicted by previously proposed thermodynamic models.