The stress concentration factor was analyzed by finite element method for the misalignment and the root configuration of welded joint with backing strip in stiffener member of steel deck plate of steel bridge, offshore structure of liner plate of power plant. Also, fatigue test was carried out by using the welded joint with misalignment, in order to investigate crack initiation and propagation in the specimen. The major findings were summarized as follows. The stress concentration factor was large at the toe as well as the root of model which had non-misalignment, but the stress concentration factor was the largest at the root of model which had misalignment by the F.E.M analysis. It was clearly that the moment was occured by misalignment because the stress concentration factor was larger and fatigue life was shorten when the misalignment became larger from the analysis and the fatigue test respectively. Therefore, the fatigue strength is improved at welded joint when misalignment was smaller. Also, the fatigue strength can be increased in welded joint with misalignment as root radius and Flank Angle become larger.