We proposed a DNA-based self-assembly method of MEMS microparticles. Single-stranded DNA exhibits a selective binding with its complementary DNA. This nature of DNA's selective binding will enable a highly regulated self-assembly when DNA is used as a binding element of assembled parts. In this study, we applied DNA self-assembly, which has been used only in nano-scale region, to MEMS microparts. MEMS microparts were disk-like Si particles with 10 μm in diameter, and 5 μm in height, with gold deposited on one surface for DNA fixing by thiol SAM (Self-assembled monolayer). DNA fixation on the gold surface and hybridization were confirmed fluorescently in aqueous condition. MEMS microparts modified with DNA were dispersed on the Si substrate with a gold surface, which was also modified with complementary DNA. After hybridization, the Si substrate with MEMS microparts were washed out by water, and the microparts with complementary DNA withstand the shear force excreted by the washing, showing enough binding force for MEMS self-assembly. The result confirmed the applicability of DNA towered MEMS self-assembly.