A new image analysis procedure for quantifying microcracks from three-dimensional (3D) X-ray microCT images of concrete is presented. The method separates microcracks from air voids and aggregates by combining filtering and morphological operations. It was applied to study the effects of supplementary cementitious materials (SCMs) and curing age on autogenous shrinkage-induced microcracks in low w/b ratio concretes, and to determine the representative elementary volume (REV) for various properties of microcracks and air voids. Results showed that slag and silica fume significantly increased autogenous shrinkage and related microcracking. These SCMs increased volume fraction, width, length, dendritic density, anisotropy, and connectivity of microcracks, but decreased specific surface and tortuosity. Similar trends were observed with age. Comparison between 3D and 2D measurements was made. REV analysis showed that a sampling volume of ~20 × 20 × 25 mm3 is sufficient for characterising most parameters of autogenous shrinkage microcracks and air voids in concrete.