Alloy nanoparticles are an important group of nanomaterials exhibiting size, shape, structure and composition dependent properties. In bulk, gold-copper alloys exhibits ordered phases Au3Cu (L12), AuCu (L10), AuCu3 (L12) [1]. Theses phases could be modified in temperature and composition at the nanoscale. For instance, ligands play an important role in the synthesis of bi-metallic nanoparticles because they influence the final shape and size of the nanoparticle. The most common method used to synthesize alloyed nanoparticles is wet-chemistry that make use of phosphoric acids, polymeric chains or thiol groups as surfactants in organic solvents such as toluene that control the spatial and shape distribution of the nanoparticles. However, the knowledge of the internal structure of the crystals provides insights to understand the crystal growth of the nanosystem. In recent years it has been reported the relationship between shape and internal features such as stacking faults and twin boundaries on nanowires and decahedral particles [2]. This features (twins, stacking faults and other defects) can modified the final shape of nanoparticles. Some other factors that affect in the same way are the concentration of the reactants and the temperature ranges. Therefore, in this work we present a systematic study on gold-copper bimetallic system to analyze the internal structure of ultrathin nanowires, decahedral nanostars and nanocubes. Modifying few conditions during the synthesis, such as metal concentrations and surfactant used, namely hexadecylamine (HDA), octadecylamine (ODA), oleylamine (OLA) or 1-dodecanethiol (DDT), we obtained Au-Cu nanocrystals with the different morphologies aforementioned. Through high resolution transmission electron microscopy (HRTEM), High Angle Annular Dark Field (HAADF) imaging and Energy Dispersive X-Ray Spectroscopy (EDS) we have obtained atomic resolution that allow us to describe the internal structure of the synthesized particles.