Herein, we describe the self-assembling of gold nanorods (GNRs) induced during the ligand exchange at their surface. An exchange reaction between tricysteine PEGylated peptidic ligands and cetyltrimethylammonium bromide (CTAB)-protected gold nanorods is conducted. We demonstrated that the terminal group charge (positively or negatively charged) and the hydrophobicity of the peptidic ligands (bearing or not an undecanoyl chain) strongly affects the self-organization of the GNRs occurring in solution. Adjusting the amount of short PEGylated peptides causes a self-organization of the gold nanorods in solution, resulting in a red- or blue-shift of the plasmon bands. The decrease of their surface charge and the self-assembling in solution were first shown by zetametry, by Dynamic Light Scattering and UV-spectroscopy. Thanks to Small Angle X-ray Scattering experiments and Transmission Electron Microscopy images, the self-organization of the nanorods in solution was clearly demonstrated and correlated to the spectroscopic change in absorbance. Conversely, in the case of longer PEGylated peptidic ligands including an undecanoyl chain, the GNRs are particularly stable against aggregation for several days after purification. By controlled drying on a substrate, we showed their ability to self-organize into well-defined ordered structures making them very attractive as building blocks to design optical materials. (C) 2014 Elsevier Inc. All rights reserved.