Atypical chronic myeloid leukemia (aCML) is an aggressive myeloid neoplasm with overlapping features of myelodysplastic syndromes (prominent granulocytic dysplasia) and myeloproliferative neoplasms (neutrophilic leukocytosis). We studied 25 molecularly-annotated and World Health Organization defined aCML patients; median age 70 years, 84% males. Cytogenetic abnormalities were seen in 36% and gene mutations in 100%. Mutational frequencies were, ASXL1 28%, TET2 16%, NRAS 16%, SETBP1 12%, RUNX1 12%, ETNK1 8% and PTPN11 4%. Fifteen patients (60%) had >1 mutation, while 9 (36%) had ≥3. The median overall survival (OS) was 10.8 months and at last follow up (median 11 months), 17 (68%) deaths and 2 (8%) leukemic transformations were documented. On univariate analysis, survival was adversely impacted by advanced age (p=0.02), low hemoglobin (p=0.01), red blood cell transfusion dependence (p=0.03), high white blood cell count (p=0.02), TET2 (p=0.03), NRAS (p=0.04), PTPN11 (p=0.02) mutations and the presence of ≥3 gene mutations (p=0.006); ASXL1, SETBP1, and ETNK1 mutations did not impact OS. In multivariable analysis, advanced age (p=0.003) [age >67: HR 10.1, 95% CI 1.3–119], low hemoglobin (p=0.008) [HB< 10gm/dl: HR 8.2, 95% CI 1.6–23.2] and TET2 mutations (p=0.01) [HR 8.8, 95% CI 1.6–47.7] retained prognostic significance. We then used age >67 years, hemoglobin <10 gm/dl and the presence of TET2 mutations (each counted as one risk factor) to create a hazard ratio weighted prognostic model; effectively stratifying patients into two risk categories, low (0–1 risk factor) and high (≥2 risk factors), with median OS of 18 and 7 months respectively.