Friction stir welding (FSW) is a solid-state joining technique initially developed for aluminium alloys. The heat generated by a rotating tool softens the material in the vicinity of the tool. The material undergoes intense plastic deformation following quite complex paths around the tool, depending on the tool geometry, process parameters and material to be welded. The comprehension of the material flow is essential to prevent voids and other internal defects which may form during welding. Several techniques have been used for tracking material flow during FSW such as metallography, the use of a marker material as a tracer or the flow visualization by FSW of dissimilar materials or even the X-ray and computer tomography. Some of these techniques are useless in the analysis of welds in homogenous materials or welds between materials of the same group. The aim of this investigation is tracking the material flow in FSW between 1mm thick sheets in aluminium alloys AA 5182-H111 and AA 6016-T4, currently used in automotive industry.