Defect formation mechanism during friction stir welding (FSW) was investigated by three-dimensional visualization of material flow around a tool. The three-dimensional flow patterns in various FSW conditions were obtained using two pairs of x-ray transmission real-time imaging systems. It revealed that the tilt of the horizontal material flow around the tool and the stagnation of the material flow at retreating side of the tool were tightly connected with the defect formation mechanism. Additionally, the material flow rates during FSW were directly calculated by the results of the three-dimensional visualization. The material flow rate at advancing side was obviously decreased in the defect formation process conditions.