Microsatellites are short repetitive sequences widespread in eukaryotic genomes. Microsatellite instability, the gain or loss of repeat units from repetitive DNA tracts caused by MisMatch Repair Deficiency (MMRD), is significant for tumor early diagnosis and prognosis. In current clinical practice, microsatellite instability detection is performed by experimental methods like MSI-PCR and MMR-IHC. With the development of next-generation sequencing technology, a number of MSI detection softwares utilizing high-throughput sequencing data have been developed. In this paper, we provide an overview on existing MSI detection methods, including experimental methods and computational methods, as well as their strengths and limits.