This study aimed to evaluate the impact of the myelodysplasia-related gene (MRG) as well as additional gene mutations on outcomes in intensively treated patients with NPM1 -mutated ( NPM1 mut ) AML. Targeted DNA sequencing of 263 genes was performed in 568 NPM1 mut AML patients (median age: 59 years) entered into the prospective AMLSG 09-09 treatment trial. Most commonly co-mutated genes were DNMT3A (49.8%), FLT3 -TKD (25.9%), PTPN11 (24.8%), NRAS (22.7%), TET2 (21.7%), IDH2 (21.3%), IDH1 (18%), and FLT3 -ITD (17.3%). MRG mutations were identified in 18.1% of cases (18-60 years: 9.8%; >60 years: 28.7%). When focusing on the 470 patients with 2022 ELN favorable-risk NPM1 mut AML, multivariable analysis for event-free survival (EFS) identified age ( p < 0.001), DNMT3A R882 ( p < 0.001), IDH1 ( p = 0.007), and MRG mutations ( p = 0.03) as unfavorable factors, cohesin gene co-mutations ( p = 0.001) and treatment with gemtuzumab ozogamicin ( p = 0.007) as favorable factors. Restricting the analysis to a subset of CR/CRi patients with available data on NPM1 mut measurable residual disease (MRD) status in blood post cycle 2 in the model, MRG mutations lost their significant effect, whereas DNMT3A R882 , MYC , and cohesin gene mutations retained the adverse and favorable effects. For OS, age ( p < 0.001), DNMT3A R882 ( p = 0.042), IDH1 ( p = 0.045), and KRAS (0.003) mutations were unfavorable factors, sole favorable factor was IDH2 co-mutation ( p = 0.037). In 2022 ELN favorable-risk NPM1 mut AML, MRG mutations are associated with inferior EFS; however, this effect is no longer present when considering NPM1 mut MRD status post cycle 2; DNMT3A R882 and MYC mutations remained adverse, and cohesin gene mutations favorable prognostic factors independent of the NPM1 mut MRD status., Competing Interests: Verena I. Gaidzik: Advisory Board: Jazz Pharmaceuticals, Abbvie, Boehringer‐Ingelheim, Speakers Bureau: Pfizer, Janssen, Abbvie, Travel Support: Abbvie. Walter Fiedler: Personal fees and non‐financial support from AbbVie; grants, personal fees, and non‐financial support from Amgen and Pfizer; and personal fees from Jazz Pharmaceuticals, Celgene, MorphoSys, Ariad/Incyte, Stemline Therapeutics, Clinigen, Daiichi Sankyo, Otsuka and Servier outside the submitted work; in addition, research support from Apis; patent issued with Amgen; support for medical writing for Amgen, Pfizer, and AbbVie. Michael W. M. Kühn: receives honoraria and is a consultant for Kura Oncology, Jazz Pharmaceuticals, Bristol‐Myers Squibb/Celgene, and Abbvie, and is on the speakers’ bureau of Gilead. Karin T. Mayer: advisory role with honoraria for Bristol Myers Squibb; Travel Support from Novartis, Celgene, Roche, Amgen, Pfizer, Jazz Pharmaceuticals, Astellas, Teva. Michael Lübbert: advisory role with honoraria from AbbVie, Astex Pharmaceuticals, Imago BioSciences, Janssen, Otsuka, Syros; Research support (to institution) from Janssen; clinical research support with study drug from Cheplapharm. Elli Papaemmanuil: founder, equity holder, and holds fiduciary roles in Isabl Inc. Felicitas Thol: advisory role with honoraria for AbbVie, BMS, Novartis, Menarini, Rigel, Astellas. Michael Heuser: declares honoraria from Abbvie, Eurocept, Jazz Pharmaceuticals, Janssen, Novartis, Takeda; paid consultancy for Abbvie, Agios, BMS, Daiichi Sankyo, Glycostem, Jazz Pharmaceuticals, Kura Oncology, Novartis, Pfizer, PinotBio, Roche, Tolremo; and research funding to his institution from Abbvie, Agios, Astellas, Bayer Pharma AG, BergenBio, Daiichi Sankyo, Glycostem, Jazz Pharmaceuticals, Loxo Oncology, Novartis, Pfizer, PinotBio, Roche. Lars Bullinger: advisory roles for Abbvie, Amgen, Astellas, Bristol‐Myers Squibb, Celgene, Daiichi Sankyo, Gilead, Hexal, Janssen, Jazz Pharmaceuticals, Menarini, Novartis, Pfizer, Sanofi, Servier; as well as research funding from Bayer, Jazz Pharmaceuticals. Hartmut Döhner: advisory role with honoraria for AbbVie, AstraZeneca, Gilead, Janssen, Jazz, Pfizer, Servier, Stemline, Syndax; clinical research funding (to institution) from AbbVie, Astellas, Bristol Myers Squibb, Celgene, Jazz Pharmaceuticals, Kronos Bio, Servier. Konstanze Döhner: consultancy with honoraria: AbbVie, Janssen, Jazz, Novartis, Bristol Myers Squibb, Celgene; Clinical Research Funding to Institution: Novartis, AbbVie, Astellas, Bristol Myers Squibb, Celgene, Jazz Pharmaceuticals, Kronos Bio, Servier. The remaining authors declare no conflicts of interest., (© 2025 The Author(s). HemaSphere published by John Wiley & Sons Ltd on behalf of European Hematology Association.)