The goal of this study was to characterize the nanostructure and the properties of starch based nanocomposites with either cellulose nano whiskers (CNW) or layered silicates (LS) (synthetic hectorite) as reinforcements. Modified potato starch was used as matrix with water and sorbitol as plasticizers and with 5 wt.% of either of the reinforcements. Two methods were explored to prepare samples for transmission electron microscopy (TEM) examination; chemical fixation and freeze etching. It was possible to characterize the nanostructure both parallel and perpendicular to the nanocomposite surface by the freeze etching technique. Both nanocomposites showed well-distributed reinforcements in the starch matrix. Dynamic mechanical thermal analysis showed that the storage modulus was significantly improved at elevated temperatures, especially for the layered silicate nanocomposite. Both nanocomposites showed a significant improvement in tensile properties compared to the pure matrix.