The present study examined HLA, KIR, and IL28B gene variant associations with an SVR following PEG-IFN and ribavirin therapy in Japanese patients with chronic hepatitis C. We found a significant association of HLA-Bw alleles with treatment outcome, although the frequency of HLA-C alleles did not differ significantly between responders and non-responders. Here, IFNL3 is linked to chronic hepatitis C virus infection.