We report a JAK2 V617F-negative case of polycythemia vera with two acquired balanced X-autosome translocations and no history of previous exposure to chemo/radiotherapy. The patient's first clone carried a novel translocation t(X;15)(q24;q13) as a sole abnormality. The second clone exhibited an additional translocation, t(X;20)(q13;q13.3), which is a rare recurrent abnormality in myeloid malignancies. This is the first report of a hematological disorder with both X chromosomes being translocated. Late replication studies revealed a switch in X-inactivation from the X chromosome involved in t(X;15) (first clone) to the X chromosome involved in the t(X;20)(q13;q13.3) (second clone). The inactivation of the translocated X chromosomes could provide potential for the inactivation of the adjacent autosomal regions, resulting in epigenetic gene silencing.