Chronic hepatitis B (CHB) is an important health problem worldwide. Relapses in CHB patients, even treated, create a major problem in patient management. The aims of this study were the detection of quantitative levels of hepatitis B virus (HBV) DNA in the sera and liver biopsy specimens of CHB patients and the comparison of the results. A total of 69 patients (49 male, 20 female; age range: 19-68 years, mean age: 36.91 +/- 11.03 years) who were prediagnosed as CHB in the Infectious Diseases and Clinical Microbiology Department of Kocaeli University (northwestern region of Turkey) were included to this prospective study. HBV-DNA levels of all of the patients were initially measured in the routine laboratory of our hospital by using a commercial real-time polymerase chain reaction (RQ-PCR; iCycler IQ System, BioRad Laboratories) and the mean HBV-DNA level (Serum DNA #2) was detected as 5.6E+6 +/- 8.5E+6 copies/mL. The mean level of ALT in CHB patients was 79.59 +/- 69.7. In our study the HBV-DNA levels of the serum and liver biopsy specimens were also measured by using an "in-house" real-time PCR (RT-PCR) (Techne Quantica, London, UK). Nucleic acid extractions were performed with the use of QlAamp DNA Mini Kit (Qiagen Inc, Hilden, Germany) according to the manufacturer's recommendations. The primers were specific for the X gene region of HBV (forward primer: 5'-TTCGCTTCACCTCTGCACG-3', reverse primer: 5'-CCCAACTCCCAGTCTTTAA-3'; probe: 5-AATGTCAACGACCGACCTT GAGGCA-pBHQ-3'). Statistical analysis was carried out with Spearman rank analysis. With the use of "in-house" real-time PCR, mean levels of HBV-DNA were found to be 8.99E+6 +/- 3.1E+7 copies/mL in the liver biopsy samples, and 4E+6 +/- 4.4E+6 copies/mL in serum samples (Serum DNA 1). There were significant positive correlations between the results obtained from in-house (Serum DNA 1) and commercial RT-PCR (Serum DNA 2) (r=0.300; p=0.024) methods. Although HBV-DNA levels in the liver tissues were found higher than those in serum samples, no correlation between the HBV-DNA levels of liver biopsy and serum samples (both serum DNA 1 and 2) was detected. This result was attributed to the standardization problems of in-house RTPCR. In conclusion, liver biopsies performed at the beginning of the therapy to detect the grade of chronic liver disease, would also be searched by means of quantitative HBV-DNA levels, however, since the determination of HBV-DNA load in liver tissues may be difficult, standardized sensitive methods should be used for this purpose.