A combination of pegylated-interferon (PEG-IFN) with ribavirin has been the choice for treating chronic hepatitis C (CHC) patients. In addition to the high cost, the treatment takes 6 to 12 months and often brings significant adverse reactions to some patients. It would therefore be beneficial to include a pre-treatment evaluation and post-treatment monitoring system to maximize the efficacy of CHC therapy. We have established a molecular diagnosis tool for assessing the efficacy of interferon combined therapy for CHC patients prior to treatment. This diagnostic tool is characterized with a prediction model consisting single nucleotide polymorphisms (SNPs) strongly associated with interferon efficacy in treating CHC patients. The prediction model has been validated by hepatitis C samples in Taiwan, and it achieved 80 % accuracy, higher than the current efficacy rates. Supplemented with the viral genotype information would further increase the prediction accuracy to 85%.