Thinning in friction stir lap joints and its relation with the process variables was investigated. Friction stir welds were made on 1 mm thick AA6111 aluminium alloy sheets in order to study the effects of rotation rate, traverse speed, plunge depth, tilt angle and pin height on faying surface defects. Sheet thinning on the advancing and retreating sides was quantified and the lap shear strength of the joints was evaluated. A decrease in the pitch of the runs at constant rotation rate increased the sheet thinning and reduced the joint strength in a linear manner. Process pitch and pin height were found to be the most critical factors in determining the faying surface lift up. A pin of the same height as the sheet thickness resulted in maximum lap shear strength. Tool tilt did not show a significant effect on the sheet thinning.