The objective of this study was to identify the frequency and types of JAK2V617F mutation in chinese patients with essential thrombocythemia (ET), to quantitatively detect the level of mutation transcripts and to investigate its clinical significance. The frequency and types of JAK2V617F mutation were detected by amplification-refractory mutation sequencing polymerase chain reaction (ARMS-PCR), the transcript level of JAK2V617F mutation was determined by using capillary electrophoresis. The results indicated that the JAK2V617F mutation was detected in 59 out of 98 patient with ET, 18 of whom were homozygous mutation. The mean age of patients with homozygous and heterozygous mutation was higher than that of patients with wild type mutation (p < 0.05). The quantitative assay using capillary electrophoresis showed that the transcript level of JAK2V617F mutation in patients with homozygous mutation was (89.9 +/- 6.7)%, which was higher than that in patients with heterozygous mutation (57.1 +/- 6.7)% (p < 0.05); the transcript level of JAK2V617F mutation in patients with age < 60 years was (62.3 +/- 16.5)%, which was lower than that in patients with age > 60 years (72.4% +/- 15.8)% (p < 0.05). The rate of thrombotic complications in patients with JAK2V617F-positive was higher than that in patients with JAK2V617F-negative in which the rate of thrombotic complication in patients with homozygous mutation was higher than that in patients with heterozygous mutation (p < 0.05). Compared with patients without thrombotic events, there were higher level of transcripts of JAK2V617F mutation in patients with thrombotic events. It is concluded that the JAK2V617F positive and negative patients with ET display the different clinical features, therefore, the analysis of mutation types and detection of transcript levels not only helps to identify the disease status and progression, but also guides the treatment of ET patients.