Background: To evaluate the predictive value of serum HBV DNA, HBV RNA, HBcrAg, HBsAg, intrahepatic HBV DNA, and cccDNA for HBeAg clearance and seroconversion during long-term treatment of nucleos(t)ide analogues (NAs) in patients with chronic hepatitis B (CHB).Method: A single center, prospective cohort of CHB patients enrolled between June 2007 and July 2008 was used for this study. Serum HBV RNA levels were retrospectively measured at baseline, 6, 12, 24, 36, 48, 60, 72, and 84 months post-NAs treatment. Serum HBsAg and HBcrAg levels were quanti ed at baseline, month 6, 60, and 72. Histological sample from liver biopsy at baseline and month 60 were analyzed for intrahepatic HBV DNA and cccDNA.Results: Eighty-three HBeAg patients were enrolled with an median follow-up time of 108 months (range 18-138 months). Of them, 53 (63.86%) patients achieved HBeAg clearance, and 37 (44.58%) achieved HBeAg seroconversion. Only baseline HBV RNA was independently associated with HBeAg clearance (OR=0.50, 95%CI 0.309-0.809, P=0.005) and seroconversion (OR=0.689, 95% CI 0.513-0.925, P=0.013). The independent negative association with HBeAg clearance and seroconversion remained for HBV RNA levels at month 6 (OR=0.42, 95%CI 0.248-0.714, P=0.001; OR=0.44, 95%CI 0.260-0.744, P=0.002) and month 12 (OR=0.39, 95%CI 0.253-0.592, P<0.001; OR=0.58, 95%CI 0.427-0.798, P=0.001). The AUC of baseline HBV RNA for predicting the HBeAg clearance and seroconversion were 0.81 (95%CI: 0.70-0.89) and 0.68 (95%CI: 0.56-0.78), respectively, higher than that of HBV DNA, HBsAg and HBcrAg. Conclusion: Lower serum HBV RNA at baseline, month 6 and 12 post NAs treatment could predict HBeAg clearance and seroconversion during long-term NAs treatment.