Radiotherapy (RT) is a central treatment modality for breast cancer patients. The purpose of this study was to investigate the DNA methylation changes in tumors following RT, and to identify epigenetic markers predicting treatment outcome. Paired biopsies from patients with inoperable breast cancer were collected both before irradiation (n=20) and after receiving 10-24 Gray (Gy) (n=19). DNA methylation analysis was performed by using Illumina Infinium 27K arrays. Fourteen genes were selected for technical validation by pyrosequencing. Eighty two differentially methylated genes were identified in irradiated (n=11) versus non-irradiated (n=19) samples (FDR=1.1%). Methylation levels in pathways belonging to the immune system were most altered after RT. Based on methylation levels before irradiation, a panel of 5 genes (H2AFY, CTSA, LTC4S, IL5RA, and RB1) were significantly associated with clinical response (p=0.041). Furthermore, the degree of methylation changes for 2516 probes correlated with the given radiation dose. Within the 2516 probes, an enrichment for pathways involved in cellular immune response, proliferation, and apoptosis was identified (FDR<5%). Here, we observed clear differences in methylation levels induced by radiation, some associated with response to treatment. The present study adds knowledge on the molecular mechanisms behind radiation response. © 2014 Wiley Periodicals, Inc.