Recently, the envelope protein 2 (E2) of hepatitis C virus (HCV) was reported to interact with double stranded RNA-dependent protein kinase (PKR) through an element homologous to the phosphorylation site of PKR and its target, eukaryotic translation initiation factor (eIF) 2alpha (PKR-eIF2alpha phosphorylation homology domain: PePHD). Inhibition of the kinase activity of PKR by this interaction was postulated as a mechanism for the resistance to interferon (IFN) therapy. The aim of this study was to clarify whether the variation of PePHD amino acid sequences affects IFN efficacy in Japanese population. Amino acid sequences of PePHD (aa. 659-670 in genotype1b, aa. 663-674 in genotype 2a and 2b) were determined in randomly selected 112 patients with chronic hepatitis C (genotype 1b; 83 patients, 2a; 14 patients, 2b; 15 patients) prior to IFN monotheray. In 21 out of the 23 genotype 1b sustained responders (SR) (91%) and 55 out of the 60 non-SR (92%), PePHD sequences were identical to that of the HCV-1b consensus sequence. Only two SR showed one amino acid substitution in PePHD, and five non-SR showed amino acid substitutions in PePHD. Among 14 genotype 2a patients, only two SR had one amino acid substitution comparing to the consensus HCV-2a sequence. Likely, only one SR had an amino acid substitution in PePHD among 15 genotype 2b patients. In conclusion, our study revealed no clinical relationship between the amino acid sequence of PePHD and the outcome of IFN therapy. PePHD polymorphism was not suggested to play a role in predicting IFN efficacy.