This study was aimed to analyze the correlation of JAK2V617F mutation burden with clinical features in patients with polycythemia vera (PV) and essential thrombocythemia (ET), The JAK2V617F mutation ratios in 47 PV samples and 43 ET samples were detected by real-time PCR. The correlation of mutation allele ratio in PV and ET samples with clinical features (hemoglobin, hematocrit, white blood cell count and platelet count) was analyzed. The results showed that the JAK2V617F mutation burden was higher in PV (0.441 +/- 0.270) than that in ET (0.209 +/- 0.192). The JAK2V617F mutation burden was positively correlated with levels of hemoglobin (PV: R = 0.518, p < 0.001; ET: R = 0.528, p = 0.005), hematocrit (PV: R = 0.510, p < 0.001; ET: R = 0.524, p = 0.005) and leukocyte (PV: R = 0.584, p = < 0.001; ET: R = 0.471, p = 0.013) in PV and ET samples. The higher JAK2V617F mutation burden was negatively correlated with levels of platelet count in PV samples (R = -0.354, p = 0.020), but there was no correlation between the JAK2V617F mutation burden and platelet count in ET samples (R = 0.233, p = 0.242). It is concluded that the higher JAK2V617F mutation burden is related with higher hemoglobin, hematocrit and leukocyte count in both PV and ET samples. The higher JAK2V617F mutation burden is correlated with lower platelet count in PV samples, but there is no correlation between JAK2V617F mutation burden and platelet count in ET samples.