Aim:To quantify hepatitis B virus (HBV) total DNA and covalently closed circular DNA (cccDNA) in liver biopsies and sera which from Chronic hepatitis B(CHB) liver cirrhosis of hepatitis B(LC) and hepatitis B relevance hepatocellular carcinoma(HCC) patients, and analysis HBV replication under the circumstances of different diseases. Methods:Total HBV DNA and cccDNA in serum and liver biopsy samples were measured in 21 CHB 23 LC and 25HCC patients by the real-time PCR assay. Results: The levels of total HBV DNA in serum,intrahepatic total HBV DNA, intrahepatic cccDNA, as well as the proportion of intrahepatic cccDNA in total HBV DNA decreased progressively in CHB,LC and HCC ,moreover CHB had significantly higher levels of total HBV DNA in serum and liver biopsy samples than LC (log [total serum HBV DNA] P = 0.024;log [total intrahepatic HBV DNA] P = 0.034); CHB and LC had significantly higher levels of intrahepatic cccDNA and the proportion of intrahepatic cccDNA in total HBV DNA than HCC(P <0.01); cccDNA couldn't be detect in all patients'serum. In CHB ,the levels of serum's total HBV DNA,intrahepatic total HBV DNA and cccDNA in HBeAg-positive group had significantly higher than the HBeAg-negative group(P <0.01) ,but in LC only intrahepatic total HBV DNA had statistical difference between HBeAg-positive and negative group (P=0.026) , no statistical difference between HBeAg-positive and negative group in HCC. Conclusions: The replication activity of hepatitis B virus in CHB,LC were higher than HCC, HBV reproduction reduced significantly in HCC. Duplication of HBV in LC was lower than CHB but had no statistical difference. The levels of HBV reproduce in HBeAg-positive group was higher than HBeAg-negative group of all three desease. 