Approximately 90% of patients with myelodysplastic syndromes (MDS) have somatic mutations in the malignant cells that are known or suspected to be oncogenic. The genetic risk-stratification of MDS has evolved substantially by the introduction of the clinical-molecular International Prognostic Scoring System (IPSS-M) that establishes next-generation sequencing at diagnosis as a standard of care. Furthermore, the International Consensus Classification (ICC) of myeloid neoplasms and acute leukemias has refined MDS diagnostic criteria with the introduction of a new myelodysplastic syndrome/acute myeloid leukemia (MDS/AML) category. Monitoring measurable residual disease (MRD) has historically been used to define remission status, improve relapse prediction, and determine the efficacy of antileukemic drugs in patients with acute and chronic leukemias. However, in contrast to leukemias, assessment of MRD including tracking of patient-specific mutations has not yet been formally defined as a biomarker for MDS. This article summarizes current evidence and challenges, and provides a conceptual framework for incorporating MRD into the treatment of MDS and future clinical trials.