Tortuosity, as being influenced by the 3D pore micro-geometry, is an important physical quantity to understand better the effect of pore structure on transport properties of cement-based materials. This study attempts to evaluate directly this pore structure-transport parameter from the microtomographic images at spatial resolution of 0.5 µm. This resolution, is by far, to our knowledge, the highest resolution reported for 3D non-invasive imaging of hardened cement pastes. The results show the feasibility of using synchrotron microtomography coupled with 3D image analysis and random walk simulation to measure the diffusion tortuosity that has a direct bearing on transport properties. The tortuosity associated with the percolating pore space seems to reflect the pore morphology that mainly controls the transport properties in young cement pastes; thus, explaining the rough agreement of the results with the computer model or experimental evidence.