Myeloproliferative neoplasms and myelodysplastic/myeloproliferative neoplasms are heterogeneous disorders. JAK2 mutation testing and karyotyping are routinely used for diagnosis but have not been incorporated into risk stratification in Philadelphia chromosome-negative myeloproliferative neoplasms. This study correlated cytogenetic abnormalities with disease stage and JAK2 status. A total of 179 cases were analyzed for the JAK2 mutation. Among them, cytogenetic data were available for 97 cases-45 of 106 JAK2+ and 52 of 73 JAK2-. The JAK2+ group showed a higher frequency of cytogenetic anomalies than the JAK2- group (23/45 [51%] vs 14/52 [27%]). Chromosome 9, chromosome 7, and 20q- were recurrent abnormalities in the JAK2+ group, whereas 13q- and trisomy 21 were common in the JAK2- group. In the JAK2+ group, chromosome 7 and complex cytogenetic abnormalities were associated with excess blasts/blastic transformation (P < .05), whereas no cases with 20q- underwent blastic transformation. Our results suggest that incorporation of JAK2 mutation testing and karyotyping allows for monitoring of disease progression with prognostic and therapeutic implications.