JAK2V617F is a common mutation in chronic myeloproliferative diseases (CMPDs). We have developed a system utilizing JAK2V617F-specific guanine quenching probe (QP-system) to detect JAK2V617F. With QP-system, results can be obtained from 100 microl of blood within 90 min. We compared QP-system with direct sequencing using 42 CMPD patients' specimens. JAK2V617F was detected in 25 specimens by QP-system, while direct sequencing failed to detect JAK2V617F in 7 of those 25. The presence of JAK2V617F mutation in these 7 specimens was confirmed by allele-specific PCR. These findings indicate that QP-system is more sensitive and useful than direct sequencing for diagnoses of CMPDs.