Interferon α (IFN­α) therapy remains a mainstay of treatment of chronic hepatitis B. However, sustained remission rates remain relatively low, and the search for factors important for response to therapy continues. In order to study the relationship between the genomic DNA methylation profile and response to interferon therapy in chronic hepatitis B, pretreatment plasma samples of 20 patients with chronic hepatitis B (CHB) receiving pegylated interferon α (PEG­IFNα) treatment were subjected to DNA methylation analyses using Roche­NimbleGen Human DNA Methylation 2.1M Deluxe Promoter v2 Array. Methylated DNA immunoprecipitation­quantitative polymerase chain reaction (MeDIP­qPCR) was used to further validate the methylation status of specific genes. A total of 588 genes were found to show differential methylation in interferon nonresponse group as compared with the rapid response group. These differential methylated genes were involved in several signaling pathways, such as the calcium signaling pathway, cell cycle and liver metabolism. The methylation levels of several genes in the two groups were confirmed by MeDIP­qPCR, consistent with the results of the MeDIP­chip study. Our data provide a foundation for future study on the functions of differential methylated genes in interferon response as well as the discovery of new molecular markers for predicting prognosis of interferon therapy in CHB patients.