Friction Stir Welding (FSW) is a complex process with several mutually interdependent parameters. A slight difference from known settings may lead to imperfections in the stirred zone. These inhomogeneities affect on the mechanical properties of the FSWed joints. In order to prevent the failure of the welded joint it is necessary to detect the most critical defects non-destructive. Especially critical defects are wormhole and lack of penetration (LOP), because of the difficulty of detection. Online thermography is used process-accompanying for defect detecting. A thermographic camera with a fixed position relating to the welding tool measures the heating-up and the cool down of the welding process. Lap joints with sound weld seam surfaces are manufactured and monitored. Different methods of evaluation of heat distribution and intensity profiles are introduced. It can be demonstrated, that it is possible to detect wormhole and lack of penetration as well as surface defects by analyzing the welding and the cooling process of friction stir welding by passive online thermography measurement. Effects of these defects on mechanical properties are shown by tensile testing.