We compared the International Prognostic Scoring System-Revised (IPSS-R) to the International Prognostic Scoring System-Molecular (IPSS-M) in 30 patients with myelodysplastic neoplasms (MDS) newly diagnosed at our institution from January 2021 to February 2023. Molecular analysis was performed by myeloid panel. The median age was 66 years (range: 35-80), and classifications were MDS-LB (n=18), MDS IB-1 (n=1), MDS IB-2 (n=2), MDS-SF3B1 (n=2), MDS-biTP53 (n=1), and MN-pCT (n=6). Each patient had 0 to 8 (median 1) mutations. The most frequently detected mutation was the TET2 mutation, and others detected in>5 patients were U2AF1, TP53, and RUNX1 mutations. IPSS-R classification indicated that 2, 14, 5, 3, and 6 patients were very low, low, intermediate (Int), high, and very high risk, respectively, whereas the IPSS-M classification indicated that 3, 9, 7, 2, 4, and 5 cases were very low, low, moderate-low (ML), moderate-high (MH), high, and very high risk, respectively. Considering IPSS-M ML and MH as the equivalent to IPSS-R Int, 13 (43%) patients had a different risk level in the IPSS-M compared to the IPSS-R. One patient was rated low-risk by IPSS-R, but reclassified as high risk by IPSS-M. It is important to be mindful of this potential for significant discrepancies between risk assessments using IPSS-R and IPSS-M in some cases when making treatment decisions.