B-lymphocyte activation is a common characteristic of chronic hepatitis B virus (HBV) infection. B cell-activating factor (BAFF) plays a crucial role in the development and activation of B lymphocytes. This study investigated serum BAFF levels in 232 patients with different clinical diseases of chronic HBV infection [33 chronic asymptomatic HBV carrier (ASC), 53 chronic hepatitis (CH), 72 liver cirrhosis (LC), and 74 hepatocellular carcinoma (HCC)] and 61 gender- and age-matched healthy controls. Serum BAFF levels in HBV patients were significantly elevated compared with healthy controls (P<0.001). HCC patients had significantly higher levels of serum BAFF than ASC, CH, and LC (all P<0.001). Serum levels of BAFF in LC were significantly higher than in ASC (P<0.001) and CH (P=0.002). Serum level of BAFF was an independent variable associated with the presence of HCC in comparison with other disease groups in multivariate analysis. The area under receiver-operating characteristic curve (AUC) value of BAFF levels was 0.914 for HCC versus ASC, 0.825 for HCC versus CH, and 0.607 for HCC versus LC, respectively. The AUC value of BAFF levels was 0.854 for LC versus ASC and 0.748 for LC versus CH, respectively. The AUC value of BAFF (0.888) for HCC was higher than that of alpha-fetoprotein (0.776). We first demonstrate that serum BAFF levels in chronic HBV infection are elevated, correlated with clinical diseases, and could be used as a biomarker for indicating disease mechanisms, activity, and diagnosis.