Experimental studies of the acoustic emission parameters distribution with structural changes in a welded joint during friction stir welding (FSW) are presented in this work. The parameters of energy, amplitude, activity and median frequency distribution of acoustic emission signals characterize the presence of features in the plasticization processes in case of disturbance of uniformity of plastic flow of a material during defect formation imitation process. An approach, based on the analysis of the parameters distribution of acoustic emission (AE), for the creation of an automated non-destructive quality control system of welded joints during FSW in real time has been proposed.