Friction stir welding is a relatively new solid-state welding process which has several superiorities over generic welding methods. In this study, aluminium alloys (AA5083-O and AA6061-T6) are selected to investigate effects of three welding variables namely tool rotation speed, tool traverse speed, and tool diameter on temperature distribution, weld width, weld depth, and heat affected zone width using finite element method. The Johnson-Cook plasticity model is implemented into Abaqus software to simulate the material plastic deformation occurring during welding process. The results demonstrated that increasing rotational speed and tool diameter lead in an increase in material temperature. Increasing traverse speed resulted in lower temperature distribution. Temperature distribution, as well as the size and shape of welding areas, are also different due to different mechanical and thermal properties. The wider heat affected zone predicted for the AA6061-T6 can be explained by its higher thermal conductivity and lower specific heat.