In this paper, A600S-T5 extruded aluminum alloy sheets which are used for floor, roof or wall panels of rail road vehicles were welded by the friction stir welding (FSW) and gas metal arc welding (GMAW) techniques. The mechanical characteristics including the tensile strength, micro-hardness and fatigue strength of the FSW joint were compared to those of the base metal and GMAW joints. In order to determine the relationship between the welding variables of FSW and the mechanical characteristics of the joint, the response function was derived using the least square method and the sensitivity analysis was performed. The rotational speed, welding speed and tilting angle of the welding tool were chosen as design variables. On the basis of the Plackett-Burman design table, eight different FSW experiments were done, and then the effects of design variables on the mechanical characteristics of the FSW joint were analyzed. The result showed that the welding speed has a most significant effect on the tensile and fatigue strength In the case of the micro-hardness, the effect of the tilting angle was the biggest.