Biodegradable nanocomposites were prepared by mixing a polymer resin and layered silicates by the melt intercalation method. Internal structure of the nanocomposite was characterized by using the small angle X-ray scattering (SAXS) and transmission electron microscope (TEM). Nanocomposites having exfoliated and intercalated structures were obtained by employing two different organically modified nanoclays. Rheological properties in shear and extensional flows and biodegradability of nanocomposites were measured. In shear flow, shear thinning behavior and increased storage modulus were observed as the clay loading increased. In extensional flow, strain hardening behavior was observed in well dispersed system. Nanocomposites with the exfoliated structure had better biodegradability than nanocomposites with the intercalated structure or pure polymer.