Next generation sequencing (NGS) has become an important tool to inform disease risk for myeloid malignancies, however data remains conflicting regarding the significance of individual mutations. We performed targeted NGS on 112 patients with AML, and 80 with MDS, who underwent allogeneic hematopoietic cell transplantation. The most common mutations in AML were TET2 (14.7%), FLT3 (12.9%), DNMT3A (12.1%), and RUNX1 (7.8%). Complex cytogenetics (HR 2.82, P = .017) and disease status (<CR) (HR 2.58, P < .001) was significantly associated with worse RFS. No individual mutation, nor variant allelic frequency (VAF), was found to be prognostic, except mutations in the RNA-splicing pathway, (HR 2.09, P = .023). Within the MDS cohort, most common mutations were ASXL1 (12.5%), SRSF2 (12%), TET2 (8.8%), and TP53 (8.8%). Complex cytogenetics (HR 5.01, P < .001), and presence of U2AF1 (HR 3.60, P = .019), was associated with worse RFS. Analysis of VAF found that TP53 and EZH2 mutations with allelic frequencies of >33% were associated with poor RFS (HR 3.57, P = .017; and HR 6.57, P = .003; respectively). Molecular profiling is increasingly important in the care of patients with AML and MDS. Further studies are needed to understand the molecular complexities, including the significance of clonal burden, to better inform care decisions.