The literature review summarizes the current knowledge of the role of molecular diagnostic techniques in optimization of chronic hepatitis C treatment algorithms. It concerns primarily hepatitis C virus genotype and plasma viral load determination before and during antiviral treatment. Despite obvious success in treating chronic hepatitis C achieved over the last several years, further optimization of treatment algorithms is still an actual problem. Among multiple known factors influencing antiviral treatment out come, viral genetic traits and dynamics of viral load during the treatment are the most important. Now the right application of current molecular diagnostic techniques already provides maximum optimization of existing antiviral treatment algorithms and achievement of high rates of sustained virologic response.