Background and Aim The presence of JAK2 V617 F was reported to be associated with JAK2 46/1 haplotype, which was considered as an independent risk factor for Budd- Chiari syndrome ( BCS) in Western countries. However, little is known in China. Therefore, the aim of this study was to determine whether the 46/1 haplotype is associated with such patients. Methods Patients with primary BCS and controls were consecutively admitted in our study from October 2009 to December 2012. The subjects were detected for the JAK2 V617 F mutation by allele-specific polymerase chain reaction ( AS- PCR) and the JAK2 46/1 haplotype by real-time PCR. Results The prevalence of JAK2 V617 F mutation was 2.37% (7/295) in BCS patients, and 46/1 haplotype was overrepresented in JAK2 V617 F-positive BCS patients compared with controls ( P < 0.01). The risk for the JAK2 V617 F-positive BCS with CC genotype was elevated compared with subjects presented TT genotype ( OR = 13.4, 95% CI = 2.01-89.5) and non- CC genotype ( OR = 15.0, 95% CI = 2.45-91.7). Conclusions Our study showed that the presence of 46/1 haplotype increased the risk of JAK2 V617 F-positive BCS in China. In addition, low prevalence of JAK2 V617 F mutation in BCS patients suggested that myeloproliferative neoplasms ( MPNs) should not be an etiological factor of BCS in China. [ABSTRACT FROM AUTHOR]