Usual rubber products are a composite from rubber and nano-filler (e.g. carbon black, silica, etc.), and it is believed that the good dispersion of the nano-filler is the most important issue determining the performance of rubber vulcanizates. So far, transmission electron microscopy (TEM) has been the most useful tool for evaluation of the dispersion. However, it affords images of the sample projected on an x, y-plane, and the information along the thickness (z-axis) direction is missing. Three-dimensional (3D) visualization of nanometer structure of nano-filler dispersion in a rubber matrix is what all rubber technologists have been dreaming of. This dream is at last realized, and described in this paper. Use of electron tomography combined with TEM (3D-TEM) enabled us to reconstruct 3D images of nano-filler aggregates in rubbery matrix. The 3D-TEM results on carbon black and silica in natural rubber were presented. Electrical resistivity of carbon black loaded natural rubber, as an example of physical properties, was measured, and explained by the structure elucidated by 3D-TEM. This technique will prove to be more and more important for the rational design of the nano-composites of rubbery matrix.