In this study we present a clean, nontoxic, environmentally friendly synthesis procedure to generate a large variety of gold nanoparticles (GNPs) by using chitosan, a biocompatible, biodegradable, natural polymer, as reducing and stabilizing agent. The formation of gold-chitosan nanocomposites was characterized by UV-vis absorption spectroscopy, transmission electron microscopy (TEM), x-ray diffraction (XRD) and Raman spectroscopy. The results show that the reaction temperature plays a crucial role in controlling the size, shape and crystalline structure of GNPs. In addition, it is demonstrated that chitosan can perform as a scaffold for the assembly of GNPs, which were successfully applied as substrate for surface-enhanced Raman scattering (SERS). To test the SERS activity, a relevant biological molecule-tryptophan-was adopted as the analyte.