Objective: To investigate the methylation status of CpG islands in the promoter region of NFAT2 gene and its relation with the NFAT2 mRNA expression in hepatocellular carcinoma (HCC) cells. Methods: The methylation status of CpG islands in the promoter region of NFAT2 in HCC and the tumor-adjacent tissues as well as in different HCC cell lines and normal hepatic cells was examined by bisulfite-sequencing PCR. NFAT2 mRNA expression in HCC and the adjacent tissues was determined by qRT-PCR, and the correlation between NFAT2 promoter methylation and its mRNA expression was analyzed. Results: The CpG island methylation rate of NFAT2 gene in HCC tissue was significantly higher than that in tumor-adjacent tissues (33.0% vs. 21.6%, P=0.003); the CpG island methylation rate of NFAT2 gene in HCC cell line HuH7, HepG2 and Hep3B was 34.8%, 40.4% and 37.0% respectively, which were all significantly higher than that in human normal hepatic cell L02 (16.2%) (all P<0.05). The NFAT2 mRNA expression in HCC tissue was significantly lower than that in tumor-adjacent tissues (0.000 602 4 vs. 0.001 469, P<0.05), and there was a negative correlation between the NFAT2 mRNA level and the degree of NFAT2 promoter methylation (r=–0.661, P=0.027). Conclusion: Down-regulated NFAT2 gene expression is probably associated with hypermethylation of CpG islands in its promoter region in HCC cells.