Objective To study the evaluation of uncertainty measurement about 2 diagnostic indexes of molecular biology.Methods According to Guidance on Evaluating the Uncertainty in Chemical Analysis Criterion,HBV-DNA and HCV-RNA internal quality control and external quality assessment specimens were detected with real-time fluorescence quantitative PCR assay,then we collected internal quality control data from April to September,2012,and external quality assessment results from 2011 to 2012.The coefficient of variations about intra-assay,inter-assay and bias were calculated,determined the standard uncertainty and the expanded uncertainty.Results In the same day,the coefficient of variation about intra-assay was 4.89% by detecting 16 HBV-DNA specimens of internal quality control,and that was 2.55% in 12 HCV-RNA detecting; the coefficient of variation of inter-assay was 9.54% by detecting 129 days HBV-DNA specimens of internal quality control from April to September,2012,and that was 5.80% by detecting 155 days HCV-RNA specimens of in temal quality control from April to September,2012; the coefficient of variation of bias about HBV-DNA and HCV-RNA were 5.33% and 6.12% by detecting 40 external quality assessment specimens distributed by national center for clinical laboratory from 2011 to 2012.After removing the data of zero,the data was recalculated as 5.83% and 7.06%.After synthesized fiactors about intra-assay,inter-assay and bias,the expanded uncertainty of HBV-DNA and HCV-RNA were 24.02% and 17.62%,and excluding the data of zero,which were 24.41% and 18.97%.Conclusions There were various influencing factors in detecting molecular biology indexes.It is digicult in mathsort and counting.Using the existing data of internal quality control and external quality assessment to evaluate the uncertainty measurement of diagnostic index about molecular biology is a rational way,which is a simple and facile method in clinical laboratory. Key words: Molecular biology; Diagnostic Index; Measurement uncertainty; Evaluation