A new method of high-resolution alpha-autoradiography using CR-39 plastics with AFM readout has been developed for the measurement of boron-compound distribution at an intracellular structure level in BNCT. Tumor cells injected by boron compound were mounted on a CR-39 plate, and irradiated by thermal neutrons. Then the plate was exposed to soft X-rays. After etching process in NaOH solution, alpha tracks from B(n,alpha) reactions and a transmission X-ray image of the cells as relief were observed simultaneously on the surface of the CR-39 with an AFM. The resolution of imaging particle tracks and cell structures is several tens of nanometers.