In this paper, the effects of irregular bead shapes on fatigue life were investigated. A modified S-N curve method was used to estimate the fatigue life, which considered the inherent multiaxiality caused by the geometrical feature produced by the welding process. The point method of the critical distance method was used to determine the fatigue effective stress. Three types of fillet joint models were tested in the fatigue experiments. For each model, real bead shapes were collected using a 3D laser scanner, and finite element analyses were performed. The results of the analyses with actual bead shapes were compared with those using an idealized bead shape model. The results of the present analytical methods showed good agreement with the experimental results.