Designing a rapid, reliable and sensitive assay, for detection of hepatitis B virus and Hepatitis C virus variants by real-time PCR, is challenging at best. A recent approach for quantifying the viral load using the sensitive fluorescence principle, was used in this study. A total of 350 samples were collected from outpatient unit, Center for Liver Research and Diagnostics (CLRD). Complete Human HBV DNA and HCV sequences were obtained from the National Centre for Biotechnology Information (NCBI); primers and probes were designed and synthesized from core, surface and x region of Hepatitis B and UTR region of HCV. Real-time based detection was done, using standard kit and in-house generated standards and RT-PCR protocols. A standard curve was generated by using the Smart Cycler II software and serial dilution 102 to 108 of cloned viral regions, the calibration curve was linear in a range from 102 to108 cp/ml for both HBV and HCV, with R2 value of 0.999 and 0.995. Out of 100 predetermined HCV negative samples, 02 samples were found positive with in-house developed RT-PCR assay, the positivity of this sample was confirmed by sequencing the amplified product. Low cost of this assay procedure and précised sample volume will permit the assay to be implemented for routine screening of Hepatitis B and C virus mono-infection and co-infection using Real Time PCR , Nucleic acid Chip technology and Fluorescent End Point detection systems. This assay is reproducible showing limited inter and intra assay variability. Our results correlated well with the standard kit for HBV and HCV virus monitor.