Short tandem repeats (STRs) are highly abundant in the human genome, but existing approaches for accurate genotyping of STRs are limited. Here, we describe a protocol for duplex molecular inversion probes for high-throughput and cost-effective STR enrichment. We have successfully tested panels targeting as many as 50K STRs in several thousands of genomic samples (e.g., HeLa cells, Du145 cells, leukemia cells, melanoma cells). However, because the protocol is plate based, the sample size is limited to a few thousand. For complete details on the use and execution of this protocol, please refer to Tao et al. (2021)., Competing Interests: The authors declare no competing interests., (© 2021 The Authors.)