External quality assessment (EQA) has been playing an increasingly important role in the implementation of nucleic acid amplification techniques (PCR) for clinical diagnosis. In this study, the results of HBV-DNA quantification and HCV-RNA detection tests evaluated by United Kingdom National External Quality Assessment Scheme for Microbiology (NEQAS) were analysed and the performance of our laboratory was evaluated. Between April 2006-January 2008, in four different distribution panels including 16 freeze-dried serum and six plasma specimens for HBV-DNA and HCV-RNA testing, respectively, were received. Viral nucleic acids were extracted by magnetic particle technology (NucliSENS-easyMAG, bioMerieux, Boxtel, Holland). HBV-DNA and HCV-RNA tests were performed by Fluorion HBV quantitative v2.0 and Fluorion HCV quantitative v2.1 (Iontek AS, Istanbul, Turkey) kits in real-time PCR (iCycler IQ v3.0a - BioRad Laboratories, Hercules, CA, USA) platform. The performance scores of all the quantification tests of HBV-DNA were 2 (completely correct result) and a strong correlation (r = 0.987) between the quantitative HBV data and the target values was found by linear regression analysis. The NEQAS scores of HCV-RNA testing, except for a false negative result (since the viral load in this specimen was very low -79 IU/ml- it was not scored by NEQAS), were 2 in all specimens. The evaluation of the data revealed 100% detection in HBV-DNA and 83.3% detection in HCV-RNA. In conclusion, the results of this study showed high accuracy of HBV quantification in the samples of HBV infected patients under antiviral therapy. However, the analytical sensitivity of HCV-RNA quantitative kit should be improved for the purpose of reliable HCV-RNA results. External quality control panels are important tools for monitoring the quality of diagnostic laboratory tests. Therefore, PCR laboratories should always have EQA in routine procedures.