Fatigue analysis of welded joints containing geometric imperfections, misalignments due to design, prefabrication and welding is discussed theoretically. Definitions, related especially to design and based on the geometric stress (hot spot stress) method are given. The accuracy and applicability of the present guidelines are discussed. A three level of accuracy procedure is introduced to analyse the fatigue life of welded structures containing misalignments. Unrecognized factors inducing bending stress concentrations and affecting the hot-spot fatigue life are introduced, such as in-plane shear stress as the reference nominal stress, location and fatigue strength of the crack initiation point. New factors to be taken into account, and new methods in a more refined stress analysis are introduced.