Hepatocellular carcinoma (HCC) is one of the most deadly malignant diseases in the world. Genetic variations in cytokine genes may have an effect on the immune and inflammatory responses which are associated with HBV-HCC. The interleukin-6 (IL-6) receptor is known to be mainly expressed by hepatocytes, neutrophils, monocytes/macrophages, and some lymphocytes, which have been used as prognostic markers in a variety of inflammatory diseases such as rheumatoid arthritis, asthma, and Crohn's disease. To determine the association of IL-6 receptor (IL-6R) polymorphism with the risk of hepatocellular carcinoma (HCC) development in the Chinese population, a hospital based case-control study was designed consisting of 192 subjects with HCC and 192 healthy control subjects. Our results revealed no risk associations (p = 0.064) with rs6684439 CT genotypes. However, rs6684439 TT genotypes were associated with a significantly decreased risk of HBV-related HCC compared with the CC genotype (odds ratio (OR) = 0.469, 95 % confidence interval (CI) 0.228-0.967, p = 0.040). The data also revealed that subjects with the T allele appeared to have a lower susceptibility to HBV-related HCC than those with the C allele (OR = 0.657, 95 % CI 0.476-0.907, p = 0.011). The present study supports the view that variants in the rs6684439 SNP of IL-6R is associated with a lower risk of HBV-related HCC, and this could provide valuable clues to understanding the mechanisms underlying susceptibility to this malignant disease. Replication and further functional studies should be carried out in the future using larger samples.