We report a novel TaqMan assay for JAK2 V617F that measures averaged copies per cell in absolute terms, as opposed to a ratio of mutant to wild-type alleles. Measurements were obtained by comparing the JAK2 V617F signal generated by the test samples to that generated by a set of external plasmid standards containing the sequence of interest. Specificity of the assay was demonstrated above 36 cycles of amplification, and endpoint titration experiments indicated sensitivity down to 0.05% clinical dilutions. The test measured linearly over a wide logarithmic range and exhibited good reproducibility. Combination of this assay with another TaqMan method for determining cell number allowed identification of 14 cases of myeloproliferative disease with greater than two copies per cell. Mutational frequency was 68% among polycythemia vera (n=44), 59% (n=37) among essential thrombocythemia and 46% (n=13) among idiopathic myelofibrosis. Levels of the mutation were significantly higher in polycythemia vera compared with essential thrombocythemia (P=0.0005) and correlated with the following jointly significant variables at diagnosis: PRV-1, hemoglobin, white cell count, neutrophil count, and red cell count, using multiple regression analyses (P=0.015). This method should be useful for assessing the relationship of gene dose to phenotype and possibly for monitoring therapy.