In this paper, it is reported a surface analysis of gold nanorods irradiated by the electron beam of a transmission electron microscope. The gold nanorods were synthesised by a bioreduction process. A transmission electron microscope was used to obtain high resolution images of the nanorod structure, which were digitally processed in order to identify the facets and surface changes. Besides, molecular simulation tools were also applied to obtain a model and to analyse the stability of these structures. Evidences of distortions were observed the (111) and (110) surfaces, which include facet reconstruction and it is shown the necessity to include the twinning of the long nanorods that looks to be a very common case.