Multi-scaled microstructures induced by natural impurities (i.e., proteins, phospholipids, carbohydrates) in natural rubber (NR) were investigated by synchrotron small-angle X-ray scattering (SAXS), wide-angle X-ray diffraction (WAXD), and optical microscopy using several kinds of untreated and chemically treated un-vulcanized samples. These microstructures include large aggregates (size less than 50 lm), well-defined crystals (size less than a few 10 lm), and micelles (size much less than 10 lm). In un-vulcanized NR samples, even though the concentrations of natural impurities are relatively low, the dispersion of these microstructures significantly affects the mechanical properties.