The Friction Stir Welding (FSW) process is a quite recent joining method whose particular characteristics yield to materials modifications not yet fully understood. This paper aims to present the research results of a study focused on the modifications induced in an aluminium alloy AA5083 – H111, when processed by FSW to build components for structural applications. The welded samples were firstly analysed by optical microscopy in order to define the different joined zones and to identify defects. Further tests included the measurement of the Vickers microhardness, grain and particle distribution and chemical analysis of the constituents, particularly of the intermetallic second phase particles, by Auger spectroscopy. Special attention has been given to the characterisation of several microstructural “non-homogeneities” like a laminated structure called onion ring and an identified anomaly (in the form of a line), whose presence was evaluated in order to determine its effects on the final joint properties. The results have shown important new details about the relationship between the microstructure and the final joint structural properties, contributing to improve the knowledge about the materials behaviour increasing the potential of utilization of the FSW process.