Summary: Three dimensional (3D) nanostructures of particulate silicas in natural rubber (NR) were observed for the first time by use of 3D transmission electron microscopy (3D‐TEM) combined with electron tomography. The method enabled us to visualize and evaluate structural characteristics in 3D space, such as the size and the volume of in situ silica generated in the NR matrix by the sol‐gel reaction of tetraethoxysilane, at nanometer scale resolution.