When a non-cylindrical probe tool is used, material adheres to the tool. This paper investigates the influence of this material on the characteristics of friction stir spot welds. This paper focuses on the material flow influenced by the material adhered to the tool. The influence of the material adhered to the tool on the mechanical properties of the friction stir spot lap joints, and on the material flow of the adhered material, is made clear. As the tool rotational speed changes, the morphology of the material adhered to the tool also changes. In a tensile-shear test, compared with the failure load of friction stir spot lap joints made using a tool without adhered material, the failure load of the friction stir spot lap joints made using a tool with adhered material is greater with a tool rotational speed of 3000 rpm, and lower with a tool rotational speed of 1000 rpm. However, the failure load of the friction stir spot lap joints is similar with tool rotational speeds of 1500 and 2250 rpm. The structural profiles are changed by the material flow, influenced by whether or not the material adheres to the tool. Also, the failure mode of the friction stir spot lap joints is different. The following patterns are observed when a tool with adhered material is used. In lower tool rotational speeds, the shear cross section is small because the stir zone is small. Also, in higher tool rotational speeds, the tensile cross section is big because the stir zone does not grow big enough to reach the surface of the upper sheet. However, from the measurement results of thrust force and torque during friction stir spot welding, it is suggested that the performance of the tool geometry does not change even if material adheres to the tool.