We propose a novel dot-pattern-projection three-dimensional (3-D) shape measurement method that can measure 3-D displacements of blink dots projected onto a measured object accurately even when it moves rapidly or is observed from a camera as moving rapidly. In our method, blinking dot patterns, in which each dot changes its size at different timings corresponding to its identification (ID) number, are projected from a projector at a high frame rate. 3-D shapes can be obtained without any miscorrespondence of the projected dots between frames by simultaneous tracking and identification of multiple dots projected onto a measured 3-D object in a camera view. Our method is implemented on a field-programmable gate array (FPGA)-based high-frame-rate (HFR) vision platform that can track and recognize as much as 15×15 blink-dot pattern in a 512×512 image in real time at 1000 fps, synchronized with an HFR projector. We demonstrate the performance of our system by showing real-time 3-D measurement results when our system is mounted on a parallel link manipulator as a sensing head.