We report various synchrotron radiation laboratory based techniques used to characterize cement based materials in nanometer scale. High resolution X-ray transmission imaging combined with a rotational axis allows for rendering of samples in three dimensions revealing volumetric details. Scanning transmission X-ray microscope combines high spatial resolution imaging with high spectral resolution of the incident beam to reveal X-ray absorption near edge structure variations in the material nanostructure. Microdiffraction scans the surface of a sample to map its high order reflection or crystallographic variations with a micron-sized incident beam. High pressure X-ray diffraction measures compressibility of pure phase materials. Unique results of studies using the above tools are discussed—a study of pores, connectivity, and morphology of a 2,000 year old concrete using nanotomography; detection of localized and varying silicate chain depolymerization in Al-substituted tobermorite, and quantification of monosulfate distribution in tricalcium aluminate hydration using scanning transmission X-ray microscopy; detection and mapping of hydration products in high volume fly ash paste using microdiffraction; and determination of mechanical properties of various AFm phases using high pressure X-ray diffraction.