Background Cancer-testis antigen (CTA) is a family of the most noticeable tumor antigens which could be potential tumor markers for cancer diagnosis. In this research we aimed to investigate the expression of SSX-1 and NY-ESO-1 mRNA, two members of the CTA family, in tissue and peripheral blood of patients with hepatocellular carcinoma (HCC) to assess their feasibility for the immunotherapy and diagnosis of HCC and the association of their expression levels with diverse clinical indicators.Methods Thirty-six north Chinese patients with HCC and 30 normal controls were enrolled in this study. Reverse transcription-polymerase chain reaction (RT-PCR) was used to detect the expression of SSX-1 and NY-ESO-1 mRNA in tumor tissues and corresponding levels in peripheral blood of patients.Results The positive rates of SSX-1 and NY-ESO-1 mRNA expression were 61.1% (22/36) and 11.1% (4/36),respectively, in cancer tissues; 38.9% (14/36) and 5.6% (2/36), respectively, in the corresponding peripheral blood samples. No positive expression of either SSX-1 or NY-ESO-1 mRNA was detected in the samples of cancer-adjacent tissues, cirrhotic tissues, normal liver tissue or the peripheral blood of control patients. No significant relationship was found between the expression of these two genes and clinical indicators such as age, gender, tumor size, extent of differentiation, serum α-fetoprotein (AFP) level or infection with hepatitis B virus (P＞0.05). The short term recurrence rate was 46.2% (6/13) in patients whose peripheral blood expressed SSX-1 mRNA, while the recurrence rate in patients with negative SSX-1 mRNA was 28.6% (4/14).Conclusions SSX-1 and NY-ESO-1 antigens might be new potentially promising targets for antigen-specific immunotherapy for HCC. High specific expression of SSX-1 and NY-ESO-1 mRNA suggested that we could apply them as tumor markers. The short term recurrence rate was significantly higher in patients whose peripheral blood expressed SSX-1 mRNA, suggesting that SSX-1 mRNA could be used as indicator for recurrence, metastasis and prognosis of HCC.