The Janus kinase 2 (JAK2) V617F mutation has considerably helped understanding of the molecular pathogenesis of chronic myeloproliferative disorders (MPD), hence this study investigated for the first time the mutational status and relative quantitation of JAK2 V617F mRNA in Chinese patients with chronic MPD. The study cohort comprised 123 chronic MPD patients (35 with polycythaemia vera [PV], 85 with essential thrombocythaemia [ET], three with idiopathic myelofibrosis [IMF]). Blood samples examined by amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) and capillary electrophoresis showed that the prevalence of the JAK2 V617F mutation was 100%, 62.4% and 66.7% in PV, ET and IMF patients, respectively. The proportion of JAK2 V617F mutated mRNA was 89.5% in homozygotes and 57.9% in heterozygotes; 18 PV heterozygous patients showed significantly higher mutated JAK2 mRNA levels than 36 heterozygous ET patients. Six of 93 patients exhibited abnormal karyotypes, but specific chromosomal abnormality was not found. The combination of ARMS-PCR and capillary electrophoresis enables quantitative assay of JAK2 V617F mutation, which helps in chronic MPD diagnosis and estimation of minimal residual disease.