Fatigue failures of bolted joints frequently lead to serious accidents in machines and structures. It is well known that fatigue failure is likely to occur around the first thread root of the bolt adjacent to the nut loaded surface and the run-out of bolt thread. That is because high stress amplitudes are generated there due to alternating external forces. Accordingly, it is significantly important to evaluate the stress amplitudes along the thread root in order to rigorously examine the fatigue failure mechanism of bolted joints. In this study, stress amplitude distributions along the thread helix including the thread run-out are analyzed by three-dimensional finite element analysis. The numerical models of the bolted joints are constructed so as to accurately represent the effect of thread helical geometry, using the modeling scheme proposed in the previous study which analyzed the stress concentrations at the thread root. The analytical objectives are bolted joints with axisymmetric geometry except for the helical-shaped threaded portions that are subjected to axisymmetric external forces. It has been substantiated, based on the stress amplitude distributions along the thread helix, which the fatigue failures are likely to originate from the first bolt thread, as in the case of the maximum stress, and the run-out of threads. It has also been shown that a bolt with reduced diameter is effective for the purpose of lowering the stress amplitude at the first thread root of bolt.